From ccb7f6b95f833f6d56e27670b84b2872b3f47998 Mon Sep 17 00:00:00 2001
From: sigven <sigven@ifi.uio.no>
Date: Tue, 30 Apr 2024 12:10:55 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20sigven/p?=
 =?UTF-8?q?harmOncoX@c9d5fffec41e50bd88d94dee5ae0694e47d87a93=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                          |   2 +-
 CODE_OF_CONDUCT.html              |   2 +-
 LICENSE-text.html                 |   2 +-
 articles/index.html               |   2 +-
 articles/pharmOncoX.html          | 169 +++++++++++++++---------------
 authors.html                      |   6 +-
 index.html                        |   2 +-
 news/index.html                   |   6 +-
 pkgdown.yml                       |   2 +-
 reference/get_biomarkers.html     |   2 +-
 reference/get_drug_records.html   |   2 +-
 reference/get_drugs.html          |   2 +-
 reference/get_targeted_drugs.html |   2 +-
 reference/index.html              |   2 +-
 reference/tidyeval.html           |   2 +-
 search.json                       |   2 +-
 16 files changed, 103 insertions(+), 104 deletions(-)

diff --git a/404.html b/404.html
index 70fc171..63b0d9c 100644
--- a/404.html
+++ b/404.html
@@ -36,7 +36,7 @@
     
     <a class="navbar-brand me-2" href="https://sigven.github.io/pharmOncoX/index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 4388780..9549a1d 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -15,7 +15,7 @@
     
     <a class="navbar-brand me-2" href="index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index dc9a688..12035c2 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -15,7 +15,7 @@
     
     <a class="navbar-brand me-2" href="index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index b228c05..2dd16f5 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -15,7 +15,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/pharmOncoX.html b/articles/pharmOncoX.html
index b4ef181..b7681b3 100644
--- a/articles/pharmOncoX.html
+++ b/articles/pharmOncoX.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -103,24 +103,19 @@ <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#i
 <span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="op">(</span><span class="st">"remotes"</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/utils/installed.packages.html" class="external-link">installed.packages</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
 <span> <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span></span>
 <span><span class="op">}</span></span>
-<span><span class="co">#&gt; Installing package into '/home/runner/work/_temp/Library'</span></span>
-<span><span class="co">#&gt; (as 'lib' is unspecified)</span></span>
 <span></span>
 <span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">'sigven/pharmOncoX'</span><span class="op">)</span></span>
 <span><span class="co">#&gt; Using github PAT from envvar GITHUB_PAT. Use `gitcreds::gitcreds_set()` and unset GITHUB_PAT in .Renviron (or elsewhere) if you want to use the more secure git credential store instead.</span></span>
 <span><span class="co">#&gt; Downloading GitHub repo sigven/pharmOncoX@HEAD</span></span>
-<span><span class="co">#&gt; cpp11 (NA -&gt; 0.4.7) [CRAN]</span></span>
-<span><span class="co">#&gt; Installing 1 packages: cpp11</span></span>
-<span><span class="co">#&gt; Installing package into '/home/runner/work/_temp/Library'</span></span>
-<span><span class="co">#&gt; (as 'lib' is unspecified)</span></span>
+<span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="color: #00BBBB;">R CMD build</span> <span style="color: #00BBBB;">─────────────────────────────────────────────────────────────────</span></span></span>
-<span><span class="co">#&gt; * checking for file ‘/tmp/Rtmpoc76Ze/remotes295c4c1b57fc/sigven-pharmOncoX-df26048/DESCRIPTION’ ... OK</span></span>
+<span><span class="co">#&gt; * checking for file ‘/tmp/RtmpuP6uPL/remotes18615796bfc/sigven-pharmOncoX-c9d5fff/DESCRIPTION’ ... OK</span></span>
 <span><span class="co">#&gt; * preparing ‘pharmOncoX’:</span></span>
 <span><span class="co">#&gt; * checking DESCRIPTION meta-information ... OK</span></span>
 <span><span class="co">#&gt; * checking for LF line-endings in source and make files and shell scripts</span></span>
 <span><span class="co">#&gt; * checking for empty or unneeded directories</span></span>
 <span><span class="co">#&gt; Omitted ‘LazyData’ from DESCRIPTION</span></span>
-<span><span class="co">#&gt; * building ‘pharmOncoX_1.6.3.tar.gz’</span></span>
+<span><span class="co">#&gt; * building ‘pharmOncoX_1.6.4.tar.gz’</span></span>
 <span><span class="co">#&gt; Installing package into '/home/runner/work/_temp/Library'</span></span>
 <span><span class="co">#&gt; (as 'lib' is unspecified)</span></span>
 <span></span>
@@ -171,24 +166,24 @@ <h3 id="get-braf-targeted-drugs-list-records-per-indication">Get BRAF-targeted d
 <span>  treatment_category <span class="op">=</span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"targeted_therapy_classified"</span>,</span>
 <span>                          <span class="st">"targeted_therapy_unclassified"</span><span class="op">)</span>,</span>
 <span>    drug_target <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'BRAF'</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:41] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:41] Object 'drug_map_name' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:41] Retrieved n = 31451 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Object 'drug_map_alias' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Retrieved n = 684962 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Object 'drug_map_basic' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Retrieved n = 31487 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Object 'drug_map_target' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Retrieved n = 39374 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Object 'drug_map_indication' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:42] Retrieved n = 62659 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:45] Record set satisfying user-defined criteria: n = 279</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:45] Collapsing record set - providing output on a 'per_drug_target_indication' resolution</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:21:45] Final record set: n = 236 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:10] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:10] Object 'drug_map_name' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:10] Retrieved n = 31451 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:10] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:10] Object 'drug_map_alias' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:10] Retrieved n = 687338 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:11] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:11] Object 'drug_map_basic' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:11] Retrieved n = 31487 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:11] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:11] Object 'drug_map_target' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:11] Retrieved n = 39374 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:11] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:11] Object 'drug_map_indication' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:11] Retrieved n = 62659 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:13] Record set satisfying user-defined criteria: n = 279</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:13] Collapsing record set - providing output on a 'per_drug_target_indication' resolution</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:13] Final record set: n = 236 records</span></span>
 <span></span>
 <span><span class="co">## Number of drug records</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">drugs</span><span class="op">$</span><span class="va">records</span><span class="op">)</span></span>
@@ -394,24 +389,24 @@ <h3 id="get-antimetabolite-drugs">Get antimetabolite drugs<a class="anchor" aria
 <span>  cache_dir <span class="op">=</span> <span class="va">cache_dir</span>, </span>
 <span>  treatment_category <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"chemo_therapy_classified"</span><span class="op">)</span>,</span>
 <span>  output_resolution <span class="op">=</span> <span class="st">"drug"</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:04] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:04] Object 'drug_map_name' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:04] Retrieved n = 31451 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Object 'drug_map_alias' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Retrieved n = 684962 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Object 'drug_map_basic' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Retrieved n = 31487 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Object 'drug_map_target' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Retrieved n = 39374 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Object 'drug_map_indication' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:05] Retrieved n = 62659 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:08] Record set satisfying user-defined criteria: n = 16503</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:08] Collapsing record set - providing output on a 'per_drug' resolution</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:08] Final record set: n = 170 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:32] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:32] Object 'drug_map_name' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:32] Retrieved n = 31451 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Object 'drug_map_alias' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Retrieved n = 687338 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Object 'drug_map_basic' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Retrieved n = 31487 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Object 'drug_map_target' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Retrieved n = 39374 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Object 'drug_map_indication' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:33] Retrieved n = 62659 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:36] Record set satisfying user-defined criteria: n = 16503</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:36] Collapsing record set - providing output on a 'per_drug' resolution</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:36] Final record set: n = 170 records</span></span>
 <span></span>
 <span><span class="va">drugs</span><span class="op">$</span><span class="va">records</span> <span class="op">&lt;-</span> <span class="va">drugs</span><span class="op">$</span><span class="va">records</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span></span>
@@ -451,24 +446,24 @@ <h3 id="get-taxanes">Get taxanes<a class="anchor" aria-label="anchor" href="#get
 <span>  cache_dir <span class="op">=</span> <span class="va">cache_dir</span>, </span>
 <span>  treatment_category <span class="op">=</span> <span class="st">"chemo_therapy_classified"</span>,</span>
 <span>  output_resolution <span class="op">=</span> <span class="st">"drug"</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:08] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:08] Object 'drug_map_name' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:08] Retrieved n = 31451 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Object 'drug_map_alias' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Retrieved n = 684962 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Object 'drug_map_basic' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Retrieved n = 31487 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Object 'drug_map_target' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Retrieved n = 39374 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Object 'drug_map_indication' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:09] Retrieved n = 62659 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:12] Record set satisfying user-defined criteria: n = 16503</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:12] Collapsing record set - providing output on a 'per_drug' resolution</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:12] Final record set: n = 170 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:36] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:36] Object 'drug_map_name' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:36] Retrieved n = 31451 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:36] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:36] Object 'drug_map_alias' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:36] Retrieved n = 687338 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:37] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:37] Object 'drug_map_basic' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:37] Retrieved n = 31487 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:37] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:37] Object 'drug_map_target' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:37] Retrieved n = 39374 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:37] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:37] Object 'drug_map_indication' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:37] Retrieved n = 62659 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:39] Record set satisfying user-defined criteria: n = 16503</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:39] Collapsing record set - providing output on a 'per_drug' resolution</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:39] Final record set: n = 170 records</span></span>
 <span></span>
 <span><span class="va">drugs</span><span class="op">$</span><span class="va">records</span> <span class="op">&lt;-</span> <span class="va">drugs</span><span class="op">$</span><span class="va">records</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span></span>
@@ -507,24 +502,24 @@ <h3 id="get-platinum-compounds">Get platinum compounds<a class="anchor" aria-lab
 <span>  cache_dir <span class="op">=</span> <span class="va">cache_dir</span>, </span>
 <span>  treatment_category <span class="op">=</span> <span class="st">"chemo_therapy_classified"</span>,</span>
 <span>  output_resolution <span class="op">=</span> <span class="st">"drug"</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:12] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:12] Object 'drug_map_name' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:12] Retrieved n = 31451 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:12] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:12] Object 'drug_map_alias' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:12] Retrieved n = 684962 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:13] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:13] Object 'drug_map_basic' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:13] Retrieved n = 31487 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:13] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:13] Object 'drug_map_target' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:13] Retrieved n = 39374 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:13] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:13] Object 'drug_map_indication' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:13] Retrieved n = 62659 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:15] Record set satisfying user-defined criteria: n = 16503</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:15] Collapsing record set - providing output on a 'per_drug' resolution</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:15] Final record set: n = 170 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Object 'drug_map_name' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Retrieved n = 31451 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Object 'drug_map_alias' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Retrieved n = 687338 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Object 'drug_map_basic' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Retrieved n = 31487 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Object 'drug_map_target' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Retrieved n = 39374 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Object 'drug_map_indication' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:40] Retrieved n = 62659 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:43] Record set satisfying user-defined criteria: n = 16503</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:43] Collapsing record set - providing output on a 'per_drug' resolution</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:43] Final record set: n = 170 records</span></span>
 <span></span>
 <span><span class="va">drugs</span><span class="op">$</span><span class="va">records</span> <span class="op">&lt;-</span> <span class="va">drugs</span><span class="op">$</span><span class="va">records</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span></span>
@@ -571,10 +566,10 @@ <h3 id="reported-associations-between-brca12-alterations-and-drug-sensitivity">R
 <code class="sourceCode R"><span></span>
 <span><span class="va">biomarkers</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/get_biomarkers.html">get_biomarkers</a></span><span class="op">(</span></span>
 <span>  cache_dir <span class="op">=</span> <span class="va">cache_dir</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:15] Downloading remote dataset from Google Drive to cache_dir</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:22] Reading from cache_dir = ' (/tmp/Rtmpoc76Ze'), argument force_download = F</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:22] Object 'biomarkers' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-04-26 12:22:22] md5 checksum is valid: 28ca0e6165547bf46b102436344a43a1</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:43] Downloading remote dataset from Google Drive to cache_dir</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:46] Reading from cache_dir = ' (/tmp/RtmpuP6uPL'), argument force_download = F</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:46] Object 'biomarkers' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-04-30 12:10:46] md5 checksum is valid: 5abd5dce7bf710c3106906a18f81f30d</span></span>
 <span></span>
 <span><span class="va">brca1_biomarkers</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="kw">for</span><span class="op">(</span><span class="va">source</span> <span class="kw">in</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'civic'</span>,<span class="st">'cgi'</span><span class="op">)</span><span class="op">)</span><span class="op">{</span></span>
@@ -628,7 +623,7 @@ <h3 id="reported-associations-between-brca12-alterations-and-drug-sensitivity">R
 <span><span class="op">)</span></span></code></pre></div>
 <p><br></p>
 <div id="htmlwidget-5b1b2f4ad92281566982" style="width:100%;height:auto;" class="datatables html-widget"></div>
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the phase 3 POLO trial patients who had germline BRCA1/2 mutation and metastatic pancreatic adenocarcinoma that had not progressed during first-line platinum-based chemotherapy were allocated to maintenance olaparib or placebo. BRCA1/2 mutation was determine by the BRAC-Analysis CDx test. Median progression free survival was significantly longer in the olaparib group than in the placebo group (7.4 months vs. 3.8 months; hazard ratio for disease progression or death, 0.53; 95% CI, 0.35 to 0.82; p=0.004). BRCA1 mutations were present in 29/92 patients in the olaparib group and 16/62 patients in the placebo group, while one patient receiving olaparib had both BRCA1 and BRCA2 germline mutations. Responses were seen in 18 (20%) patients in the olaparib group, including two complete responses. The safety profile of olaparib was similar to that observed in other patient populations.","Report of OlympiA (NCT02032823), a randomized, double-blind, placebo-controlled study of 1836 patients with HER2-negative breast cancer with germline pathogenic or likely pathogenic mutations in BRCA1 or BRCA2. Patients were early stage but had completed chemotherapy; ER/PR+ patients could also have concurrent hormone therapy. 82% of patients were triple negative. 72% of patients had BRCA1 germline mutations, 27% had BRCA2, and 0.4% both. 921 patients received olaparib and 915 placebo.  Invasive disease-free survival (IDFS) showed improvement with olaparib treatment (86% vs 77%, HR 0.58 [0.41 to 0.82], P<0.001). For overall survival, deaths in the olaparib arm were lower (59 vs 86, HR 0.68 [0.44 to 1.05], P=0.02). The IDFS benefit was independent of whether mutation was in BRCA1 (HR=0.52, 0.39-0.70) or BRCA2 (HR 0.52, 0.30-0.86).","Report of OlympiA (NCT02032823), a randomized, double-blind, placebo-controlled study of 1836 patients with HER2-negative breast cancer with germline pathogenic or likely pathogenic mutations in BRCA1 or BRCA2. Patients were early stage but had completed chemotherapy; ER/PR+ patients could also have concurrent hormone therapy. 82% of patients were triple negative. 72% of patients had BRCA1 germline mutations, 27% had BRCA2, and 0.4% both. 921 patients received olaparib and 915 placebo. Invasive disease-free survival (IDFS) showed improvement with olaparib treatment (86% vs 77%, HR 0.58 [0.41 to 0.82], P<0.001). For overall survival, deaths in the olaparib arm were lower (59 vs 86, HR 0.68 [0.44 to 1.05], P=0.02). The IDFS benefit was independent of whether mutation was in BRCA1 (HR=0.52, 0.39-0.70) or BRCA2 (HR 0.52, 0.30-0.86).","In the phase 3 POLO trial patients who had germline BRCA1/2 mutation and metastatic pancreatic adenocarcinoma that had not progressed during first-line platinum-based chemotherapy were allocated to maintenance olaparib or placebo. BRCA1/2 mutation was determine by the BRAC-Analysis CDx test. Median progression free survival was significantly longer in the olaparib group than in the placebo group (7.4 months vs. 3.8 months; hazard ratio for disease progression or death, 0.53; 95% CI, 0.35 to 0.82; p=0.004). BRCA2 mutations were present in 62/92 patients in the olaparib group and 46/62 patients in the placebo group, while one patient receiving olaparib had both BRCA1 and BRCA2 germline mutations. Responses were seen in 18 (20%) patients in the olaparib group, including two complete responses. The safety profile of olaparib was similar to that observed in other patient populations.","Report of OlympiA (NCT02032823), a randomized, double-blind, placebo-controlled study of 1836 patients with HER2-negative breast cancer with germline pathogenic or likely pathogenic mutations in BRCA1 or BRCA2. Patients were early stage but had completed chemotherapy; ER/PR+ patients could also have concurrent hormone therapy. 82% of patients were triple negative. 72% of patients had BRCA1 germline mutations, 27% had BRCA2, and 0.4% both. 921 patients received olaparib and 915 placebo.  Invasive disease-free survival (IDFS) showed improvement with olaparib treatment (86% vs 77%, HR 0.58 [0.41 to 0.82], P<0.001). For overall survival, deaths in the olaparib arm were lower (59 vs 86, HR 0.68 [0.44 to 1.05], P=0.02). The IDFS benefit was independent of whether mutation was in BRCA1 (HR=0.52, 0.39-0.70) or BRCA2 (HR 0.52, 0.30-0.86).","Report of OlympiA (NCT02032823), a randomized, double-blind, placebo-controlled study of 1836 patients with HER2-negative breast cancer with germline pathogenic or likely pathogenic mutations in BRCA1 or BRCA2. Patients were early stage but had completed chemotherapy; ER/PR+ patients could also have concurrent hormone therapy. 82% of patients were triple negative. 72% of patients had BRCA1 germline mutations, 27% had BRCA2, and 0.4% both. 921 patients received olaparib and 915 placebo. Invasive disease-free survival (IDFS) showed improvement with olaparib treatment (86% vs 77%, HR 0.58 [0.41 to 0.82], P<0.001). For overall survival, deaths in the olaparib arm were lower (59 vs 86, HR 0.68 [0.44 to 1.05], P=0.02). The IDFS benefit was independent of whether mutation was in BRCA1 (HR=0.52, 0.39-0.70) or BRCA2 (HR 0.52, 0.30-0.86).","In the phase 3 SOLO1 trial 390 patients with newly diagnosed advanced ovarian cancer with a mutation in BRCA1 or BRCA2 who had complete or partial response after platinum-based chemotherapy were randomized 2:1 to receive olaparib or placebo. The olaparib arm had 191 patients with BRCA1 mutation, 66 BRCA2, and 3 patients with both BRCA1 and BRCA2, while the placebo arm had 91 BRCA1 and 40 BRCA2 mutant patients. Analysis of PFS by blinded independent review found freedom from disease progression or death at 3 years was 69% in the olaparib arm compared with 35% in the placebo arm (hazard ratio for disease progression or death, 0.28; 95% CI, 0.20 to 0.39; P<0.001).","In the phase 3 SOLO1 trial 390 patients with newly diagnosed advanced ovarian cancer with a mutation in BRCA1 or BRCA2 who had complete or partial response after platinum-based chemotherapy were randomized 2:1 to receive olaparib or placebo. Two patients were found to have somatic BRCA1/2 mutations. Analysis of PFS by blinded independent review found freedom from disease progression or death at 3 years was 69% in the olaparib arm compared with 35% in the placebo arm (hazard ratio for disease progression or death, 0.28; 95% CI, 0.20 to 0.39; P<0.001).","Combined meta-analysis of Study 10 (NCT01482715, phase I/II) and ARIEL2 (NCT01891344, phase II), both multi-centre, open-label, single-arm trials evaluating rucaparib in ovarian cancer with BRCA1 or BRCA2 deleterious germline or somatic mutations. Mutation status was determined by local testing or by central Foundation Medicine sequencing. Of 106 patients, OR was 53.8% (95% CI, 43.8-63.5); 8.5% and 45.3% of patients achieved complete and partial responses, respectively. Median duration of response was 9.2 months (95% CI, 6.6-11.6). Response rates by gene/mutation: BRCA1/2 germline (n=88, OR 53.4); BRCA1/2 somatic (n=18, OR 55.6); BRCA1 (n=67, OR 53.7); BRCA2 (n=39, OR 53.8).","Combined meta-analysis of Study 10 (NCT01482715, phase I/II) and ARIEL2 (NCT01891344, phase II), both multi-centre, open-label, single-arm trials evaluating rucaparib in ovarian cancer with BRCA1 or BRCA2 deleterious germline or somatic mutations. Mutation status was determined by local testing or by central Foundation Medicine sequencing. Of 106 patients, OR was 53.8% (95% CI, 43.8-63.5); 8.5% and 45.3% of patients achieved complete and partial responses, respectively. Median duration of response was 9.2 months (95% CI, 6.6-11.6). Response rates by gene/mutation: BRCA1/2 germline (n=88, OR 53.4); BRCA1/2 somatic (n=18, OR 55.6); BRCA1 (n=67, OR 53.7); BRCA2 (n=39, OR 53.8).","This randomized, open-label, phase 3 trial evaluated the PARP inhibitor olaparib in 387 men with metastatic castration-resistant prostate cancer (mCRPC) who had disease progression while receiving a new hormonal agent (e.g., enzalutamide or abiraterone). The study found that in men with mCRPC who had somatic or germline deleterious alterations (irrespective of zygosity) in any of the following HRR genes (BRCA1, BRCA2, ATM, BRIP1, BARD1, CDK12, CHEK1, CHEK2, FANCL, PALB2, PPP2R2A, RAD51B, RAD51C, RAD51D, and RAD54L), olaparib was associated with longer progression-free survival and better measures of response and patient-reported end points than either enzalutamide or abiraterone (PFS HR 0.49 [0.38, 0.63]). For 15 patients with BRCA1 mutations specifically, PFS HR 0.41 [0.13-1.39]. . Based on the results of this study, on May 19, 2020, the Food and Drug Administration approved olaparib (LYNPARZA) for adult patients with deleterious or suspected deleterious germline or somatic HRR gene-mutated mCRPC, who have progressed following prior treatment with enzalutamide or abiraterone.","In the phase 3 SOLO1 trial 390 patients with newly diagnosed advanced ovarian cancer with a mutation in BRCA1 or BRCA2 who had complete or partial response after platinum-based chemotherapy were randomized 2:1 to receive olaparib or placebo. The olaparib arm had 191 patients with BRCA1 mutation, 66 BRCA2, and 3 patients with both BRCA1 and BRCA2, while the placebo arm had 91 BRCA1 and 40 BRCA2 mutant patients. Analysis of PFS by blinded independent review found freedom from disease progression or death at 3 years was 69% in the olaparib arm compared with 35% in the placebo arm (hazard ratio for disease progression or death, 0.28; 95% CI, 0.20 to 0.39; P<0.001).","In phase 3 trial of 387 patients comparing olaparib and new hormonal agent (enzalutamide or abiraterone) therapy for patients with metastatic castration-resistant prostate cancer harboring homologous recombinant repair-related gene mutation detected from a tumor sample, olaparib showed significant PFS benefit in an ITT population (HR [95%CI] 0.49 [0.38, 0.63]). But in subgroup analysis, the treatment effect differed in each mutated genes. Among them, patients with BRCA2 mutations (olaparib: n=92, control: n=53) showed a prominent benefit of olaparib (PFS HR [95%CI] 0.21 [0.13, 0.32]).","Combined meta-analysis of Study 10 (NCT01482715, phase I/II) and ARIEL2 (NCT01891344, phase II), both multi-centre, open-label, single-arm trials evaluating rucaparib in ovarian cancer with BRCA1 or BRCA2 deleterious germline or somatic mutations. Mutation status was determined by local testing or by central Foundation Medicine sequencing. Of 106 patients, OR was 53.8% (95% CI, 43.8-63.5); 8.5% and 45.3% of patients achieved complete and partial responses, respectively. Median duration of response was 9.2 months (95% CI, 6.6-11.6). Response rates by gene/mutation: BRCA1/2 germline (n=88, OR 53.4); BRCA1/2 somatic (n=18, OR 55.6); BRCA1 (n=67, OR 53.7); BRCA2 (n=39, OR 53.8).","Combined meta-analysis of Study 10 (NCT01482715, phase I/II) and ARIEL2 (NCT01891344, phase II), both multi-centre, open-label, single-arm trials evaluating rucaparib in ovarian cancer with BRCA1 or BRCA2 deleterious germline or somatic mutations. Mutation status was determined by local testing or by central Foundation Medicine sequencing. Of 106 patients, OR was 53.8% (95% CI, 43.8-63.5); 8.5% and 45.3% of patients achieved complete and partial responses, respectively. Median duration of response was 9.2 months (95% CI, 6.6-11.6). Response rates by gene/mutation: BRCA1/2 germline (n=88, OR 53.4); BRCA1/2 somatic (n=18, OR 55.6); BRCA1 (n=67, OR 53.7); BRCA2 (n=39, OR 53.8).",null,null,null,null,null,null,null,null,null,null,"The combination of PARP inhibition (Olaparib) with BRCA mutation results in irreparable and lethal DNA damage. Response rates are higher in BRCA1 mutation positive women with high grade serous or undifferentiated ovarian cancer.","In part 2 of a two-part dose-escalation phase I trial (NCT01286987), 71 patients with Ewings sarcoma, breast, ovarian, small cell lung, or pancreatic cancers received 1.0 mg/day talazoparib treatment. Of patients with BRCA mutation-associated breast and ovarian cancers, confirmed responses were observed in 7 of 14 (50%) and 5 of 12 (42%) patients, respectively.","In part 2 of a two-part dose-escalation phase I trial (NCT01286987), 71 patients with Ewings sarcoma, breast, ovarian, small cell lung, or pancreatic cancers received 1.0 mg/day talazoparib treatment. Of patients with BRCA mutation-associated breast and ovarian cancers, confirmed responses were observed in 7 of 14 (50%) and 5 of 12 (42%) patients, respectively.","302 patients (234 with progression events) with HER2-negative metastatic breast cancer and with a confirmed deleterious or suspected deleterious germline BRCA mutation (164 BRCA1, 129 BRCA2) had significantly improved progression-free survival and better response rate to olaparib (PARP inhibitor) than standard therapy (7.0 mo vs 4.2 mo, hazard ratio 0.58, 95% CI 0.43-0.8) in this randomized phase 3 trial (NCT02000622). For BRCA1 patients specifically, the hazard ratio was 0.54, 95% CI 0.37-0.79).","The combination of PARP inhibition (Olaparib) with BRCA mutation results in irreparable and lethal DNA damage. Response rates are higher in BRCA2 mutation positive women with high grade serous or undifferentiated ovarian cancer.","In a phase 2 trial of patients with metastatic, castration-resistant prostate cancer, treated with olaparib tablets at a dose of 400 mg twice a day, all 7 patients harbouring BRCA2 loss of function alleles (biallelic somatic loss or germline mutations in combination with somatic copy loss or copy neutral LOH) demonstrated a clinical response.","In part 2 of a two-part dose-escalation phase I trial (NCT01286987), 71 patients with Ewings sarcoma, breast, ovarian, small cell lung, or pancreatic cancers received 1.0 mg/day talazoparib treatment. Of patients with BRCA mutation-associated breast and ovarian cancers, confirmed responses were observed in 7 of 14 (50%) and 5 of 12 (42%) patients, respectively.","In part 2 of a two-part dose-escalation phase I trial (NCT01286987), 71 patients with Ewings sarcoma, breast, ovarian, small cell lung, or pancreatic cancers received 1.0 mg/day talazoparib treatment. Of patients with BRCA mutation-associated breast and ovarian cancers, confirmed responses were observed in 7 of 14 (50%) and 5 of 12 (42%) patients, respectively.","302 patients (234 with progression events) with HER2-negative metastatic breast cancer and with a confirmed deleterious or suspected deleterious germline BRCA mutation (164 BRCA1, 129 BRCA2) had significantly improved progression-free survival and better response rate to olaparib (PARP inhibitor) than standard therapy (7.0 mo vs 4.2 mo, hazard ratio 0.58, 95% CI 0.43-0.8) in this randomized phase 3 trial (NCT02000622). For BRCA2 patients specifically, the hazard ratio was 0.68, 95% CI 0.45-0.1.07.","In this phase 1 trial, 60 patients with advanced solid tumors (ovarian, breast, colorectal, melanoma, sarcoma, prostate) were treated with PARP inhibitor olaparib. Durable antitumor activity was only observed in BRCA1/2 mutation carriers. 19 BRCA carriers had ovarian, breast, or prostate cancers; 12 of these (63%) had a clinical benefit from treatment with olaparib: radiologic or tumor-marker responses or meaningful disease stabilization (stable disease for a period of 4 months or more). Nine BRCA carriers had a response according to RECIST, with the response sustained for more than 76 weeks in one patient. No responses were seen in patients without BRCA mutation.","In a study of ovarian carcinomas, 81% of tumors with germline BRCA1/2 mutations were platinum sensitive, whereas only 60% of tumors with non-BRCA1/2 mutations were platinum sensitive (N=47; N=158; P=0.01). Sensitivity was defined by maintenance of complete response greater than 6 months post platinum-based therapy.","In a study of ovarian carcinomas, 87% of tumors with somatic BRCA1/2 mutations were platinum sensitive, whereas only 60% of tumors with non-BRCA1/2 mutations were platinum sensitive (N=38; N=158; P=0.002). Sensitivity to platinum was defined by maintenance of complete response greater than 6 months post platinum-based therapy.","46 women with platinum-sensitive, high-grade, BRCA1/2+ ovarian cancer received either olaparib monotherapy or olaparib/cediranib combination therapy.  Median PFS was increased in combination therapy (17.7 months versus 9.0 months; HR=0.42; 95%CI 0.23-0.76; p=0.005); overall response rate was increased in the combination therapy (79.6% versus 47.8%; p=0.002); and total deaths were reduced in combination therapy (6 patients versus 10 patients).","In an evaluation of 77 patients, those who had BRCA1/2 germline mutations (n=11) had an increase response rate to cisplatin when compared to those without germline mutations (54.5% versus 19.7%; P=0.022) although progression free survival and overall survival was not significantly different.","In a study of 63 patients with ovarian cancer, 17 patients had BRCA1 or BRCA2 mutations and 46 patients had no BRCA mutations.  Of the BRCA-positive patients, 7/17(41%; 95%CI 22-64) showed objective response to olaparib whereas only 11/46 BRCA-negative patients (24%; 95%CI 14-38) showed objective response to olaparib.","In a study of 26 patients with breast cancer, 10 patients were BRCA-positive and 16 patients were BRCA-negative.  Regardless of BRCA status, none showed objective response when treated with olaparib.","A phase 2 trial on patients with relapsed, platinum-sensitive high grade ovarian, fallopian tube or primary peritoneal carcinoma (ARIEL2 Part1, NCT01891344) was held to assess PARP inhibitor rucaparib on 3 genetically defined subsets of patients. Out of 40 BRCA mutant (BRCA1 or BRCA2) patients, 14 had homozygous somatic BRCA1 mutation or deletion. Confirmed objective response was seen in 71% (10/14) of the somatic BRCA1 mutant subgroup. Authors note that response rate was similar regardless of whether the BRCA mutation was somatic or germline, in BRCA 1 or BRCA 2. In a BRCA wild-type subgroup, with low levels of loss of heterozygosity (LOH), confirmed objective response was observed in 10% (7/70) of the patients. Patients with BRCA mutant tumors experienced significantly longer median progression free survival than patients with BRCA wildtype, LOH low tumors (12.8 vs 5.2 mo, HR: 0.27, P<0.0001).","Randomized, open-label, phase 3 trial in which olaparib monotherapy was compared with standard therapy in patients with a germline BRCA mutation HER2–negative metastatic breast cancer. 205 patients were assigned to receive olaparib and 97 were assigned to receive standard therapy. Median progression-free survival was significantly longer in the olaparib group than in the standard-therapy group (7.0 months vs. 4.2 months; hazard ratio 0.58; 95%CI 0.43 to 0.80; P<0.001). A response to treatment occurred in 100 of the 167 patients who had measurable disease in the olaparib group (59.9%; 95% CI, 52.0 to 67.4) and in 19 of the 66 patients in the standard-therapy group (28.8%; 95% CI, 18.3 to 41.3). A complete response was seen in 9.0% of the patients who had measurable disease in the olaparib group and in 1.5% in the standard-therapy group.","Twenty-three patients with pancreatic cancer havoring BRCA1/2 germline mutations received olaparib. Five (21.7%) patients had a BRCA1 mutation. All but one had received prior gemcitabine, and 65% had received prior platinum. Tumor response rate was 21.7% and stable disease more than 8 weeks was 35%.","Patients with BRCA1/2 associated pancreatic adenocarcinoma were evaluated retrospectively. In patients with stage 3 and 4, the median overall survival (mOS) was 22 months for the platinum exposed (n=22), compared with 9 months for the non-platinum (n=21) treatment groups (p<0.039)","In Phase I study for pancreatic cancer patients GEM 600 mg/m2 + CDDP 25 mg/m2 + Veliparib 20 - 80 mg twice daily showed response rate of  77.8% (7/9) and mOS of 23.3 months in germline BRCA mutation-positive patients with stage IV disease.","Veliparib 400mg BID was administered to patients with germline BRCA1/2-mutated pancreatic cancer. Sixteen patients were enrolled. All except two (12.5%) had previously been treated with platinum therapy. No confirmed partial response was observed. One patient who had received prior single-agent gemcitabine only had an unconfirmed PR.","A phase 2 trial on patients with relapsed, platinum-sensitive high grade ovarian, fallopian tube or primary peritoneal carcinoma (ARIEL2 Part1, NCT01891344) was held to assess PARP inhibitor rucaparib on 3 genetically defined subsets of patients. Out of 40 BRCA (BRCA1 or BRCA2) mutant patients, 14 had germline BRCA1 mutation, 13 of which were homozygous mutation and one with unknown zygosity. Confirmed objective response was seen in 86% (12/14) of the germline BRCA1 mutant subgroup. Authors note that response rate was similar regardless of whether the BRCA mutation was somatic or germline, in BRCA 1 or BRCA 2. In a BRCA wild-type subgroup, with low levels of loss of heterozygosity (LOH), confirmed objective response was observed in 10% (7/70) of the patients. Patients with BRCA mutant tumors experienced significantly longer median progression free survival than patients with BRCA wildtype, LOH low tumors (12.8 vs 5.2 mo, HR: 0.27, P<0.0001).","In this phase 1 trial 60 patients with advanced solid tumors (ovarian, breast, colorectal, melanoma, sarcoma, prostate) were treated with PARP inhibitor olaparib. Durable antitumor activity was only observed in BRCA1/2 mutation carriers.19 BRCA carriers had ovarian, breast, or prostate cancers; 12 of these (63%) had a clinical benefit from treatment with olaparib: radiologic or tumor-marker responses or meaningful disease stabilization (stable disease for a period of 4 months or more). Nine BRCA carriers had a response according to RECIST, with the response sustained for more than 76 weeks in one patient. No responses were seen in patients without BRCA mutation.","In a study of ovarian carcinomas, 81% of tumors with germline BRCA1/2 mutations were platinum sensitive, whereas only 60% of tumors with non-BRCA1/2 mutations were platinum sensitive (N=47; N=158; P=0.01). Sensitivity was defined by maintenance of complete response greater than 6 months post platinum-based therapy.","In a study of ovarian carcinomas, 87% of tumors with somatic BRCA1/2 mutations were platinum sensitive, whereas only 60% of tumors with non-BRCA1/2 mutations were platinum sensitive (N=38; N=158; P=0.002). Sensitivity to platinum was defined by maintenance of complete response greater than 6 months post platinum therapy.","46 women with platinum-sensitive, high-grade, BRCA1/2+ ovarian cancer received either olaparib monotherapy or olaparib/cediranib combination therapy.  Median PFS was increased in combination therapy (17.7 months versus 9.0 months; HR=0.42; 95%CI 0.23-0.76; p=0.005); overall response rate was increased in the combination therapy (79.6% versus 47.8%; p=0.002); and total deaths were reduced in combination therapy (6 patients versus 10 patients).","In an evaluation of 77 patients, those who had BRCA1/2 germline mutations (n=11) had an increase response rate to cisplatin when compared to those without germline mutations (54.5% versus 19.7%; P=0.022) although progression free survival and overall survival was not significantly different.","In a study of 63 patients with ovarian cancer, 17 patients had BRCA1 or BRCA2 mutations and 46 patients had no BRCA mutations.  Of the BRCA-positive patients, 7/17(41%; 95%CI 22-64) showed objective response to olaparib whereas only 11/46 BRCA-negative patients (24%; 95%CI 14-38) showed objective response to olaparib.","In a study of 26 patients with breast cancer, 10 patients were BRCA-positive and 16 patients were BRCA-negative.  Regardless of BRCA status, none showed objective response when treated with olaparib.","A phase 2 trial on patients with relapsed, platinum-sensitive high grade ovarian, fallopian tube or primary peritoneal carcinoma (ARIEL2 Part1, NCT01891344) was held to assess PARP inhibitor rucaparib on 3 genetically defined subsets of patients. Out of 40 BRCA (BRCA1 or BRCA2) mutant patients, 5 had somatic BRCA2 mutation, 4 of which were homozygous mutations and one had unknown zygosity. Confirmed objective response was seen in 80% (4/5) of the somatic BRCA2 mutant subgroup. Authors note that response rate was similar regardless of whether the BRCA mutation was somatic or germline, in BRCA 1 or BRCA 2. In a BRCA wild-type subgroup, with low levels of loss of heterozygosity (LOH), confirmed objective response was observed in 10% (7/70) of the patients. Patients with BRCA mutant tumors experienced significantly longer median progression free survival than patients with BRCA wildtype, LOH low tumors (12.8 vs 5.2 mo, HR: 0.27, P<0.0001).","Randomized, open-label, phase 3 trial in which olaparib monotherapy was compared with standard therapy in patients with a germline BRCA mutation HER2–negative metastatic breast cancer. 205 patients were assigned to receive olaparib and 97 were assigned to receive standard therapy. Median progression-free survival was significantly longer in the olaparib group than in the standard-therapy group (7.0 months vs. 4.2 months; hazard ratio 0.58; 95%CI 0.43 to 0.80; P<0.001). A response to treatment occurred in 100 of the 167 patients who had measurable disease in the olaparib group (59.9%; 95% CI, 52.0 to 67.4) and in 19 of the 66 patients in the standard-therapy group (28.8%; 95% CI, 18.3 to 41.3). A complete response was seen in 9.0% of the patients who had measurable disease in the olaparib group and in 1.5% in the standard-therapy group.","Twenty-three patients with pancreatic cancer havoring BRCA1/2 germline mutations received olaparib. Eighteen (78%) patients had a BRCA2 mutation.  In total of patients with BRCA1/2 mutation , all but one had received prior gemcitabine, and 65% had received prior platinum. Tumor response rate was 21.7% and stable disease more than 8 weeks was 35%.","Patients with BRCA1/2 associated pancreatic adenocarcinoma were evaluated retrospectively. In patients with stage 3 and 4, the median overall survival (mOS) was 22 months for the platinum exposed (n=22), compared with 9 months for the non-platinum (n=21) treatment groups (p<0.039)","In Phase I study for pancreatic cancer patients GEM 600 mg/m2 + CDDP 25 mg/m2 + Veliparib 20 - 80 mg twice daily showed response rate of  77.8% (7/9) and mOS of 23.3 months in germline BRCA mutation-positive patients with stage IV disease.","Veliparib 400mg bid was administered to patients with germline BRCA1/2 mutated pancreatic cancer. Sixteen pts was enrolled. All except two pts (12.5%) had previously been treated with platinum therapy. No confirmed PR was observed. One patient who had received prior single-agent gemcitabine only had an unconfirmed PR.","A phase 2 trial on patients with relapsed, platinum-sensitive high grade ovarian, fallopian tube or primary peritoneal carcinoma (ARIEL2 Part1, NCT01891344) was held to assess PARP inhibitor rucaparib on 3 genetically defined subsets of patients. Out of 40 BRCA (BRCA1 or BRCA2) mutant patients, 6 had germline homozygous BRCA2 mutation. Confirmed objective response was seen in 83% (5/6) of the germline BRCA2 mutant subgroup. Authors note that response rate was similar regardless of whether the BRCA mutation was somatic or germline, in BRCA 1 or BRCA 2. In a BRCA wild-type subgroup, with low levels of loss of heterozygosity (LOH), confirmed objective response was observed in 10% (7/70) of the patients. Patients with BRCA mutant tumors experienced significantly longer median progression free survival than patients with BRCA wildtype, LOH low tumors (12.8 vs 5.2 mo, HR: 0.27, P<0.0001).","Absent/low expression of BRCA1 (IHC) was associated with improved response to chemotherapy in 292 patients with sporadic ovarian cancer compared to patients with high expression (odds ratio 2.47: 95%CI 1.10-5.55, p=0.029).","1/1 patients with BRCA1 homozygous deletion had a response to olaparib in this phase 2 study.","Patient with germline BRCA2 mutation underwent resection of pancreatic cancer. Around three years later, tumor recurrence was detected by MRI and PET-CT confirmed it. She was treated with gemcitabine plus iniparib in clinical trial. Excellent response to therapy was observed and surgery was performed but no residual tumor tissue was detected","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a case report, a 3‐year‐old girl with glioblastoma harboring a probable germline heterozygous BRCA2 Lys3326Ter (K3326*) nonsense variant. After debulking surgery, the patient received standard‐of‐care treatment with radiation and temozolomide. Nine months later the PARP inhibitor olaparib was administered in combination with temozolomide for 16 cycles. This regimen was well tolerated by the patient and serial imaging showed a reduction in tumor size.",null,null,null,null,"The authors show that in the CX-5461 and CX-3543, G-quadruplex stabilizing agents, demonstrate specific toxicity against BRCA deficient breast cancer derived cells and polyclonal patient-derived xenograft models. Xenografts harbored both a germline BRCA and a somatic BRCA mutation leading to disruption of both. The BRCA and NHEJ pathways are required for the repair of CX-5461 and CX-3543-induced DNA damage and failure to do so leads to lethality.","In pancreatic cell lines PL11 (FANCC-deficient) and CAPAN1 (BRCA2-mutated), sensitivity to DNA cross-linking agents was observed compared to FANCC/BRCA2 wildtype cell lines (Su86.86, CFPAC, AsPc1, and MiaPaCa2). Mitomycin C specifically led to regression in 8/11 xenografts of the CAPAN1 cell line compared to 2/9 in the CFPAC (BRCA2 wildtype) cell line.","The authors show that in the CX-5461 and CX-3543, G-quadruplex stabilizing agents, demonstrate specific toxicity against BRCA deficient breast cancer derived cells and polyclonal patient-derived xenograft models. The BRCA and NHE J pathways are required for the repair of CX-5461 and CX-3543-induced DNA damage and failure to do so leads to lethality.","Expression of BRCA1 in 6 mesothelioma cell lines was associated with sensitivity to vinorelbine in functional studies.","In an in vitro study, a SNU-251 cell line expressing BRCA1 W1815X truncating mutation demonstrated increased sensitivity to olaparib treatment with long-term exposure, compared to ovarian cell lines expressing BRCA1 wild-type. Sensitivity was determined by assessing cytotoxicity and doubling time. The authors note that the slow doubling time of SNU-251 cells was compensated for with a 2 week cytotoxicity assay as compared to the 1 week assay used for all other cell lines.",null,null],["Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Resistance","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity","Sensitivity"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>variant_name<\/th>\n      <th>primary_site<\/th>\n      <th>therapeutic_context<\/th>\n      <th>molecular_profile_name<\/th>\n      <th>evidence_level<\/th>\n      <th>variant_id<\/th>\n      <th>evidence_type<\/th>\n      <th>biomarker_source<\/th>\n      <th>biomarker_source_datestamp<\/th>\n      <th>evidence_id<\/th>\n      <th>variant_origin<\/th>\n      <th>literature_id<\/th>\n      <th>evidence_url<\/th>\n      <th>evidence_description<\/th>\n      <th>clinical_significance<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"buttons":["csv","excel"],"dom":"Bfrtip","columnDefs":[{"className":"dt-right","targets":6},{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"variant_name","targets":1},{"name":"primary_site","targets":2},{"name":"therapeutic_context","targets":3},{"name":"molecular_profile_name","targets":4},{"name":"evidence_level","targets":5},{"name":"variant_id","targets":6},{"name":"evidence_type","targets":7},{"name":"biomarker_source","targets":8},{"name":"biomarker_source_datestamp","targets":9},{"name":"evidence_id","targets":10},{"name":"variant_origin","targets":11},{"name":"literature_id","targets":12},{"name":"evidence_url","targets":13},{"name":"evidence_description","targets":14},{"name":"clinical_significance","targets":15}],"order":[],"autoWidth":false,"orderClasses":false,"responsive":true}},"evals":[],"jsHooks":[]}</script><p><br><br></p>
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the phase 3 POLO trial patients who had germline BRCA1/2 mutation and metastatic pancreatic adenocarcinoma that had not progressed during first-line platinum-based chemotherapy were allocated to maintenance olaparib or placebo. BRCA1/2 mutation was determine by the BRAC-Analysis CDx test. Median progression free survival was significantly longer in the olaparib group than in the placebo group (7.4 months vs. 3.8 months; hazard ratio for disease progression or death, 0.53; 95% CI, 0.35 to 0.82; p=0.004). BRCA1 mutations were present in 29/92 patients in the olaparib group and 16/62 patients in the placebo group, while one patient receiving olaparib had both BRCA1 and BRCA2 germline mutations. Responses were seen in 18 (20%) patients in the olaparib group, including two complete responses. The safety profile of olaparib was similar to that observed in other patient populations.","Report of OlympiA (NCT02032823), a randomized, double-blind, placebo-controlled study of 1836 patients with HER2-negative breast cancer with germline pathogenic or likely pathogenic mutations in BRCA1 or BRCA2. Patients were early stage but had completed chemotherapy; ER/PR+ patients could also have concurrent hormone therapy. 82% of patients were triple negative. 72% of patients had BRCA1 germline mutations, 27% had BRCA2, and 0.4% both. 921 patients received olaparib and 915 placebo.  Invasive disease-free survival (IDFS) showed improvement with olaparib treatment (86% vs 77%, HR 0.58 [0.41 to 0.82], P<0.001). For overall survival, deaths in the olaparib arm were lower (59 vs 86, HR 0.68 [0.44 to 1.05], P=0.02). The IDFS benefit was independent of whether mutation was in BRCA1 (HR=0.52, 0.39-0.70) or BRCA2 (HR 0.52, 0.30-0.86).","Report of OlympiA (NCT02032823), a randomized, double-blind, placebo-controlled study of 1836 patients with HER2-negative breast cancer with germline pathogenic or likely pathogenic mutations in BRCA1 or BRCA2. Patients were early stage but had completed chemotherapy; ER/PR+ patients could also have concurrent hormone therapy. 82% of patients were triple negative. 72% of patients had BRCA1 germline mutations, 27% had BRCA2, and 0.4% both. 921 patients received olaparib and 915 placebo. Invasive disease-free survival (IDFS) showed improvement with olaparib treatment (86% vs 77%, HR 0.58 [0.41 to 0.82], P<0.001). For overall survival, deaths in the olaparib arm were lower (59 vs 86, HR 0.68 [0.44 to 1.05], P=0.02). The IDFS benefit was independent of whether mutation was in BRCA1 (HR=0.52, 0.39-0.70) or BRCA2 (HR 0.52, 0.30-0.86).","In the phase 3 POLO trial patients who had germline BRCA1/2 mutation and metastatic pancreatic adenocarcinoma that had not progressed during first-line platinum-based chemotherapy were allocated to maintenance olaparib or placebo. BRCA1/2 mutation was determine by the BRAC-Analysis CDx test. Median progression free survival was significantly longer in the olaparib group than in the placebo group (7.4 months vs. 3.8 months; hazard ratio for disease progression or death, 0.53; 95% CI, 0.35 to 0.82; p=0.004). BRCA2 mutations were present in 62/92 patients in the olaparib group and 46/62 patients in the placebo group, while one patient receiving olaparib had both BRCA1 and BRCA2 germline mutations. Responses were seen in 18 (20%) patients in the olaparib group, including two complete responses. The safety profile of olaparib was similar to that observed in other patient populations.","Report of OlympiA (NCT02032823), a randomized, double-blind, placebo-controlled study of 1836 patients with HER2-negative breast cancer with germline pathogenic or likely pathogenic mutations in BRCA1 or BRCA2. Patients were early stage but had completed chemotherapy; ER/PR+ patients could also have concurrent hormone therapy. 82% of patients were triple negative. 72% of patients had BRCA1 germline mutations, 27% had BRCA2, and 0.4% both. 921 patients received olaparib and 915 placebo.  Invasive disease-free survival (IDFS) showed improvement with olaparib treatment (86% vs 77%, HR 0.58 [0.41 to 0.82], P<0.001). For overall survival, deaths in the olaparib arm were lower (59 vs 86, HR 0.68 [0.44 to 1.05], P=0.02). The IDFS benefit was independent of whether mutation was in BRCA1 (HR=0.52, 0.39-0.70) or BRCA2 (HR 0.52, 0.30-0.86).","Report of OlympiA (NCT02032823), a randomized, double-blind, placebo-controlled study of 1836 patients with HER2-negative breast cancer with germline pathogenic or likely pathogenic mutations in BRCA1 or BRCA2. Patients were early stage but had completed chemotherapy; ER/PR+ patients could also have concurrent hormone therapy. 82% of patients were triple negative. 72% of patients had BRCA1 germline mutations, 27% had BRCA2, and 0.4% both. 921 patients received olaparib and 915 placebo. Invasive disease-free survival (IDFS) showed improvement with olaparib treatment (86% vs 77%, HR 0.58 [0.41 to 0.82], P<0.001). For overall survival, deaths in the olaparib arm were lower (59 vs 86, HR 0.68 [0.44 to 1.05], P=0.02). The IDFS benefit was independent of whether mutation was in BRCA1 (HR=0.52, 0.39-0.70) or BRCA2 (HR 0.52, 0.30-0.86).","In the phase 3 SOLO1 trial 390 patients with newly diagnosed advanced ovarian cancer with a mutation in BRCA1 or BRCA2 who had complete or partial response after platinum-based chemotherapy were randomized 2:1 to receive olaparib or placebo. The olaparib arm had 191 patients with BRCA1 mutation, 66 BRCA2, and 3 patients with both BRCA1 and BRCA2, while the placebo arm had 91 BRCA1 and 40 BRCA2 mutant patients. Analysis of PFS by blinded independent review found freedom from disease progression or death at 3 years was 69% in the olaparib arm compared with 35% in the placebo arm (hazard ratio for disease progression or death, 0.28; 95% CI, 0.20 to 0.39; P<0.001).","In the phase 3 SOLO1 trial 390 patients with newly diagnosed advanced ovarian cancer with a mutation in BRCA1 or BRCA2 who had complete or partial response after platinum-based chemotherapy were randomized 2:1 to receive olaparib or placebo. Two patients were found to have somatic BRCA1/2 mutations. Analysis of PFS by blinded independent review found freedom from disease progression or death at 3 years was 69% in the olaparib arm compared with 35% in the placebo arm (hazard ratio for disease progression or death, 0.28; 95% CI, 0.20 to 0.39; P<0.001).","Combined meta-analysis of Study 10 (NCT01482715, phase I/II) and ARIEL2 (NCT01891344, phase II), both multi-centre, open-label, single-arm trials evaluating rucaparib in ovarian cancer with BRCA1 or BRCA2 deleterious germline or somatic mutations. Mutation status was determined by local testing or by central Foundation Medicine sequencing. Of 106 patients, OR was 53.8% (95% CI, 43.8-63.5); 8.5% and 45.3% of patients achieved complete and partial responses, respectively. Median duration of response was 9.2 months (95% CI, 6.6-11.6). Response rates by gene/mutation: BRCA1/2 germline (n=88, OR 53.4); BRCA1/2 somatic (n=18, OR 55.6); BRCA1 (n=67, OR 53.7); BRCA2 (n=39, OR 53.8).","Combined meta-analysis of Study 10 (NCT01482715, phase I/II) and ARIEL2 (NCT01891344, phase II), both multi-centre, open-label, single-arm trials evaluating rucaparib in ovarian cancer with BRCA1 or BRCA2 deleterious germline or somatic mutations. Mutation status was determined by local testing or by central Foundation Medicine sequencing. Of 106 patients, OR was 53.8% (95% CI, 43.8-63.5); 8.5% and 45.3% of patients achieved complete and partial responses, respectively. Median duration of response was 9.2 months (95% CI, 6.6-11.6). Response rates by gene/mutation: BRCA1/2 germline (n=88, OR 53.4); BRCA1/2 somatic (n=18, OR 55.6); BRCA1 (n=67, OR 53.7); BRCA2 (n=39, OR 53.8).","This randomized, open-label, phase 3 trial evaluated the PARP inhibitor olaparib in 387 men with metastatic castration-resistant prostate cancer (mCRPC) who had disease progression while receiving a new hormonal agent (e.g., enzalutamide or abiraterone). The study found that in men with mCRPC who had somatic or germline deleterious alterations (irrespective of zygosity) in any of the following HRR genes (BRCA1, BRCA2, ATM, BRIP1, BARD1, CDK12, CHEK1, CHEK2, FANCL, PALB2, PPP2R2A, RAD51B, RAD51C, RAD51D, and RAD54L), olaparib was associated with longer progression-free survival and better measures of response and patient-reported end points than either enzalutamide or abiraterone (PFS HR 0.49 [0.38, 0.63]). For 15 patients with BRCA1 mutations specifically, PFS HR 0.41 [0.13-1.39]. . Based on the results of this study, on May 19, 2020, the Food and Drug Administration approved olaparib (LYNPARZA) for adult patients with deleterious or suspected deleterious germline or somatic HRR gene-mutated mCRPC, who have progressed following prior treatment with enzalutamide or abiraterone.","In the phase 3 SOLO1 trial 390 patients with newly diagnosed advanced ovarian cancer with a mutation in BRCA1 or BRCA2 who had complete or partial response after platinum-based chemotherapy were randomized 2:1 to receive olaparib or placebo. The olaparib arm had 191 patients with BRCA1 mutation, 66 BRCA2, and 3 patients with both BRCA1 and BRCA2, while the placebo arm had 91 BRCA1 and 40 BRCA2 mutant patients. Analysis of PFS by blinded independent review found freedom from disease progression or death at 3 years was 69% in the olaparib arm compared with 35% in the placebo arm (hazard ratio for disease progression or death, 0.28; 95% CI, 0.20 to 0.39; P<0.001).","In phase 3 trial of 387 patients comparing olaparib and new hormonal agent (enzalutamide or abiraterone) therapy for patients with metastatic castration-resistant prostate cancer harboring homologous recombinant repair-related gene mutation detected from a tumor sample, olaparib showed significant PFS benefit in an ITT population (HR [95%CI] 0.49 [0.38, 0.63]). But in subgroup analysis, the treatment effect differed in each mutated genes. Among them, patients with BRCA2 mutations (olaparib: n=92, control: n=53) showed a prominent benefit of olaparib (PFS HR [95%CI] 0.21 [0.13, 0.32]).","Combined meta-analysis of Study 10 (NCT01482715, phase I/II) and ARIEL2 (NCT01891344, phase II), both multi-centre, open-label, single-arm trials evaluating rucaparib in ovarian cancer with BRCA1 or BRCA2 deleterious germline or somatic mutations. Mutation status was determined by local testing or by central Foundation Medicine sequencing. Of 106 patients, OR was 53.8% (95% CI, 43.8-63.5); 8.5% and 45.3% of patients achieved complete and partial responses, respectively. Median duration of response was 9.2 months (95% CI, 6.6-11.6). Response rates by gene/mutation: BRCA1/2 germline (n=88, OR 53.4); BRCA1/2 somatic (n=18, OR 55.6); BRCA1 (n=67, OR 53.7); BRCA2 (n=39, OR 53.8).","Combined meta-analysis of Study 10 (NCT01482715, phase I/II) and ARIEL2 (NCT01891344, phase II), both multi-centre, open-label, single-arm trials evaluating rucaparib in ovarian cancer with BRCA1 or BRCA2 deleterious germline or somatic mutations. Mutation status was determined by local testing or by central Foundation Medicine sequencing. Of 106 patients, OR was 53.8% (95% CI, 43.8-63.5); 8.5% and 45.3% of patients achieved complete and partial responses, respectively. Median duration of response was 9.2 months (95% CI, 6.6-11.6). Response rates by gene/mutation: BRCA1/2 germline (n=88, OR 53.4); BRCA1/2 somatic (n=18, OR 55.6); BRCA1 (n=67, OR 53.7); BRCA2 (n=39, OR 53.8).",null,null,null,null,null,null,null,null,null,null,"The combination of PARP inhibition (Olaparib) with BRCA mutation results in irreparable and lethal DNA damage. Response rates are higher in BRCA1 mutation positive women with high grade serous or undifferentiated ovarian cancer.","In part 2 of a two-part dose-escalation phase I trial (NCT01286987), 71 patients with Ewings sarcoma, breast, ovarian, small cell lung, or pancreatic cancers received 1.0 mg/day talazoparib treatment. Of patients with BRCA mutation-associated breast and ovarian cancers, confirmed responses were observed in 7 of 14 (50%) and 5 of 12 (42%) patients, respectively.","In part 2 of a two-part dose-escalation phase I trial (NCT01286987), 71 patients with Ewings sarcoma, breast, ovarian, small cell lung, or pancreatic cancers received 1.0 mg/day talazoparib treatment. Of patients with BRCA mutation-associated breast and ovarian cancers, confirmed responses were observed in 7 of 14 (50%) and 5 of 12 (42%) patients, respectively.","302 patients (234 with progression events) with HER2-negative metastatic breast cancer and with a confirmed deleterious or suspected deleterious germline BRCA mutation (164 BRCA1, 129 BRCA2) had significantly improved progression-free survival and better response rate to olaparib (PARP inhibitor) than standard therapy (7.0 mo vs 4.2 mo, hazard ratio 0.58, 95% CI 0.43-0.8) in this randomized phase 3 trial (NCT02000622). For BRCA1 patients specifically, the hazard ratio was 0.54, 95% CI 0.37-0.79).","The combination of PARP inhibition (Olaparib) with BRCA mutation results in irreparable and lethal DNA damage. Response rates are higher in BRCA2 mutation positive women with high grade serous or undifferentiated ovarian cancer.","In a phase 2 trial of patients with metastatic, castration-resistant prostate cancer, treated with olaparib tablets at a dose of 400 mg twice a day, all 7 patients harbouring BRCA2 loss of function alleles (biallelic somatic loss or germline mutations in combination with somatic copy loss or copy neutral LOH) demonstrated a clinical response.","In part 2 of a two-part dose-escalation phase I trial (NCT01286987), 71 patients with Ewings sarcoma, breast, ovarian, small cell lung, or pancreatic cancers received 1.0 mg/day talazoparib treatment. Of patients with BRCA mutation-associated breast and ovarian cancers, confirmed responses were observed in 7 of 14 (50%) and 5 of 12 (42%) patients, respectively.","In part 2 of a two-part dose-escalation phase I trial (NCT01286987), 71 patients with Ewings sarcoma, breast, ovarian, small cell lung, or pancreatic cancers received 1.0 mg/day talazoparib treatment. Of patients with BRCA mutation-associated breast and ovarian cancers, confirmed responses were observed in 7 of 14 (50%) and 5 of 12 (42%) patients, respectively.","302 patients (234 with progression events) with HER2-negative metastatic breast cancer and with a confirmed deleterious or suspected deleterious germline BRCA mutation (164 BRCA1, 129 BRCA2) had significantly improved progression-free survival and better response rate to olaparib (PARP inhibitor) than standard therapy (7.0 mo vs 4.2 mo, hazard ratio 0.58, 95% CI 0.43-0.8) in this randomized phase 3 trial (NCT02000622). For BRCA2 patients specifically, the hazard ratio was 0.68, 95% CI 0.45-0.1.07.","In this phase 1 trial, 60 patients with advanced solid tumors (ovarian, breast, colorectal, melanoma, sarcoma, prostate) were treated with PARP inhibitor olaparib. Durable antitumor activity was only observed in BRCA1/2 mutation carriers. 19 BRCA carriers had ovarian, breast, or prostate cancers; 12 of these (63%) had a clinical benefit from treatment with olaparib: radiologic or tumor-marker responses or meaningful disease stabilization (stable disease for a period of 4 months or more). Nine BRCA carriers had a response according to RECIST, with the response sustained for more than 76 weeks in one patient. No responses were seen in patients without BRCA mutation.","In a study of ovarian carcinomas, 81% of tumors with germline BRCA1/2 mutations were platinum sensitive, whereas only 60% of tumors with non-BRCA1/2 mutations were platinum sensitive (N=47; N=158; P=0.01). Sensitivity was defined by maintenance of complete response greater than 6 months post platinum-based therapy.","In a study of ovarian carcinomas, 87% of tumors with somatic BRCA1/2 mutations were platinum sensitive, whereas only 60% of tumors with non-BRCA1/2 mutations were platinum sensitive (N=38; N=158; P=0.002). Sensitivity to platinum was defined by maintenance of complete response greater than 6 months post platinum-based therapy.","46 women with platinum-sensitive, high-grade, BRCA1/2+ ovarian cancer received either olaparib monotherapy or olaparib/cediranib combination therapy.  Median PFS was increased in combination therapy (17.7 months versus 9.0 months; HR=0.42; 95%CI 0.23-0.76; p=0.005); overall response rate was increased in the combination therapy (79.6% versus 47.8%; p=0.002); and total deaths were reduced in combination therapy (6 patients versus 10 patients).","In an evaluation of 77 patients, those who had BRCA1/2 germline mutations (n=11) had an increase response rate to cisplatin when compared to those without germline mutations (54.5% versus 19.7%; P=0.022) although progression free survival and overall survival was not significantly different.","In a study of 63 patients with ovarian cancer, 17 patients had BRCA1 or BRCA2 mutations and 46 patients had no BRCA mutations.  Of the BRCA-positive patients, 7/17(41%; 95%CI 22-64) showed objective response to olaparib whereas only 11/46 BRCA-negative patients (24%; 95%CI 14-38) showed objective response to olaparib.","In a study of 26 patients with breast cancer, 10 patients were BRCA-positive and 16 patients were BRCA-negative.  Regardless of BRCA status, none showed objective response when treated with olaparib.","A phase 2 trial on patients with relapsed, platinum-sensitive high grade ovarian, fallopian tube or primary peritoneal carcinoma (ARIEL2 Part1, NCT01891344) was held to assess PARP inhibitor rucaparib on 3 genetically defined subsets of patients. Out of 40 BRCA mutant (BRCA1 or BRCA2) patients, 14 had homozygous somatic BRCA1 mutation or deletion. Confirmed objective response was seen in 71% (10/14) of the somatic BRCA1 mutant subgroup. Authors note that response rate was similar regardless of whether the BRCA mutation was somatic or germline, in BRCA 1 or BRCA 2. In a BRCA wild-type subgroup, with low levels of loss of heterozygosity (LOH), confirmed objective response was observed in 10% (7/70) of the patients. Patients with BRCA mutant tumors experienced significantly longer median progression free survival than patients with BRCA wildtype, LOH low tumors (12.8 vs 5.2 mo, HR: 0.27, P<0.0001).","Randomized, open-label, phase 3 trial in which olaparib monotherapy was compared with standard therapy in patients with a germline BRCA mutation HER2–negative metastatic breast cancer. 205 patients were assigned to receive olaparib and 97 were assigned to receive standard therapy. Median progression-free survival was significantly longer in the olaparib group than in the standard-therapy group (7.0 months vs. 4.2 months; hazard ratio 0.58; 95%CI 0.43 to 0.80; P<0.001). A response to treatment occurred in 100 of the 167 patients who had measurable disease in the olaparib group (59.9%; 95% CI, 52.0 to 67.4) and in 19 of the 66 patients in the standard-therapy group (28.8%; 95% CI, 18.3 to 41.3). A complete response was seen in 9.0% of the patients who had measurable disease in the olaparib group and in 1.5% in the standard-therapy group.","Twenty-three patients with pancreatic cancer havoring BRCA1/2 germline mutations received olaparib. Five (21.7%) patients had a BRCA1 mutation. All but one had received prior gemcitabine, and 65% had received prior platinum. Tumor response rate was 21.7% and stable disease more than 8 weeks was 35%.","Patients with BRCA1/2 associated pancreatic adenocarcinoma were evaluated retrospectively. In patients with stage 3 and 4, the median overall survival (mOS) was 22 months for the platinum exposed (n=22), compared with 9 months for the non-platinum (n=21) treatment groups (p<0.039)","In Phase I study for pancreatic cancer patients GEM 600 mg/m2 + CDDP 25 mg/m2 + Veliparib 20 - 80 mg twice daily showed response rate of  77.8% (7/9) and mOS of 23.3 months in germline BRCA mutation-positive patients with stage IV disease.","Veliparib 400mg BID was administered to patients with germline BRCA1/2-mutated pancreatic cancer. Sixteen patients were enrolled. All except two (12.5%) had previously been treated with platinum therapy. No confirmed partial response was observed. One patient who had received prior single-agent gemcitabine only had an unconfirmed PR.","A phase 2 trial on patients with relapsed, platinum-sensitive high grade ovarian, fallopian tube or primary peritoneal carcinoma (ARIEL2 Part1, NCT01891344) was held to assess PARP inhibitor rucaparib on 3 genetically defined subsets of patients. Out of 40 BRCA (BRCA1 or BRCA2) mutant patients, 14 had germline BRCA1 mutation, 13 of which were homozygous mutation and one with unknown zygosity. Confirmed objective response was seen in 86% (12/14) of the germline BRCA1 mutant subgroup. Authors note that response rate was similar regardless of whether the BRCA mutation was somatic or germline, in BRCA 1 or BRCA 2. In a BRCA wild-type subgroup, with low levels of loss of heterozygosity (LOH), confirmed objective response was observed in 10% (7/70) of the patients. Patients with BRCA mutant tumors experienced significantly longer median progression free survival than patients with BRCA wildtype, LOH low tumors (12.8 vs 5.2 mo, HR: 0.27, P<0.0001).","In this phase 1 trial 60 patients with advanced solid tumors (ovarian, breast, colorectal, melanoma, sarcoma, prostate) were treated with PARP inhibitor olaparib. Durable antitumor activity was only observed in BRCA1/2 mutation carriers.19 BRCA carriers had ovarian, breast, or prostate cancers; 12 of these (63%) had a clinical benefit from treatment with olaparib: radiologic or tumor-marker responses or meaningful disease stabilization (stable disease for a period of 4 months or more). Nine BRCA carriers had a response according to RECIST, with the response sustained for more than 76 weeks in one patient. No responses were seen in patients without BRCA mutation.","In a study of ovarian carcinomas, 81% of tumors with germline BRCA1/2 mutations were platinum sensitive, whereas only 60% of tumors with non-BRCA1/2 mutations were platinum sensitive (N=47; N=158; P=0.01). Sensitivity was defined by maintenance of complete response greater than 6 months post platinum-based therapy.","In a study of ovarian carcinomas, 87% of tumors with somatic BRCA1/2 mutations were platinum sensitive, whereas only 60% of tumors with non-BRCA1/2 mutations were platinum sensitive (N=38; N=158; P=0.002). Sensitivity to platinum was defined by maintenance of complete response greater than 6 months post platinum therapy.","46 women with platinum-sensitive, high-grade, BRCA1/2+ ovarian cancer received either olaparib monotherapy or olaparib/cediranib combination therapy.  Median PFS was increased in combination therapy (17.7 months versus 9.0 months; HR=0.42; 95%CI 0.23-0.76; p=0.005); overall response rate was increased in the combination therapy (79.6% versus 47.8%; p=0.002); and total deaths were reduced in combination therapy (6 patients versus 10 patients).","In an evaluation of 77 patients, those who had BRCA1/2 germline mutations (n=11) had an increase response rate to cisplatin when compared to those without germline mutations (54.5% versus 19.7%; P=0.022) although progression free survival and overall survival was not significantly different.","In a study of 63 patients with ovarian cancer, 17 patients had BRCA1 or BRCA2 mutations and 46 patients had no BRCA mutations.  Of the BRCA-positive patients, 7/17(41%; 95%CI 22-64) showed objective response to olaparib whereas only 11/46 BRCA-negative patients (24%; 95%CI 14-38) showed objective response to olaparib.","In a study of 26 patients with breast cancer, 10 patients were BRCA-positive and 16 patients were BRCA-negative.  Regardless of BRCA status, none showed objective response when treated with olaparib.","A phase 2 trial on patients with relapsed, platinum-sensitive high grade ovarian, fallopian tube or primary peritoneal carcinoma (ARIEL2 Part1, NCT01891344) was held to assess PARP inhibitor rucaparib on 3 genetically defined subsets of patients. Out of 40 BRCA (BRCA1 or BRCA2) mutant patients, 5 had somatic BRCA2 mutation, 4 of which were homozygous mutations and one had unknown zygosity. Confirmed objective response was seen in 80% (4/5) of the somatic BRCA2 mutant subgroup. Authors note that response rate was similar regardless of whether the BRCA mutation was somatic or germline, in BRCA 1 or BRCA 2. In a BRCA wild-type subgroup, with low levels of loss of heterozygosity (LOH), confirmed objective response was observed in 10% (7/70) of the patients. Patients with BRCA mutant tumors experienced significantly longer median progression free survival than patients with BRCA wildtype, LOH low tumors (12.8 vs 5.2 mo, HR: 0.27, P<0.0001).","Randomized, open-label, phase 3 trial in which olaparib monotherapy was compared with standard therapy in patients with a germline BRCA mutation HER2–negative metastatic breast cancer. 205 patients were assigned to receive olaparib and 97 were assigned to receive standard therapy. Median progression-free survival was significantly longer in the olaparib group than in the standard-therapy group (7.0 months vs. 4.2 months; hazard ratio 0.58; 95%CI 0.43 to 0.80; P<0.001). A response to treatment occurred in 100 of the 167 patients who had measurable disease in the olaparib group (59.9%; 95% CI, 52.0 to 67.4) and in 19 of the 66 patients in the standard-therapy group (28.8%; 95% CI, 18.3 to 41.3). A complete response was seen in 9.0% of the patients who had measurable disease in the olaparib group and in 1.5% in the standard-therapy group.","Twenty-three patients with pancreatic cancer havoring BRCA1/2 germline mutations received olaparib. Eighteen (78%) patients had a BRCA2 mutation.  In total of patients with BRCA1/2 mutation , all but one had received prior gemcitabine, and 65% had received prior platinum. Tumor response rate was 21.7% and stable disease more than 8 weeks was 35%.","Patients with BRCA1/2 associated pancreatic adenocarcinoma were evaluated retrospectively. In patients with stage 3 and 4, the median overall survival (mOS) was 22 months for the platinum exposed (n=22), compared with 9 months for the non-platinum (n=21) treatment groups (p<0.039)","In Phase I study for pancreatic cancer patients GEM 600 mg/m2 + CDDP 25 mg/m2 + Veliparib 20 - 80 mg twice daily showed response rate of  77.8% (7/9) and mOS of 23.3 months in germline BRCA mutation-positive patients with stage IV disease.","Veliparib 400mg bid was administered to patients with germline BRCA1/2 mutated pancreatic cancer. Sixteen pts was enrolled. All except two pts (12.5%) had previously been treated with platinum therapy. No confirmed PR was observed. One patient who had received prior single-agent gemcitabine only had an unconfirmed PR.","A phase 2 trial on patients with relapsed, platinum-sensitive high grade ovarian, fallopian tube or primary peritoneal carcinoma (ARIEL2 Part1, NCT01891344) was held to assess PARP inhibitor rucaparib on 3 genetically defined subsets of patients. Out of 40 BRCA (BRCA1 or BRCA2) mutant patients, 6 had germline homozygous BRCA2 mutation. Confirmed objective response was seen in 83% (5/6) of the germline BRCA2 mutant subgroup. Authors note that response rate was similar regardless of whether the BRCA mutation was somatic or germline, in BRCA 1 or BRCA 2. In a BRCA wild-type subgroup, with low levels of loss of heterozygosity (LOH), confirmed objective response was observed in 10% (7/70) of the patients. Patients with BRCA mutant tumors experienced significantly longer median progression free survival than patients with BRCA wildtype, LOH low tumors (12.8 vs 5.2 mo, HR: 0.27, P<0.0001).","Absent/low expression of BRCA1 (IHC) was associated with improved response to chemotherapy in 292 patients with sporadic ovarian cancer compared to patients with high expression (odds ratio 2.47: 95%CI 1.10-5.55, p=0.029).","1/1 patients with BRCA1 homozygous deletion had a response to olaparib in this phase 2 study.","Patient with germline BRCA2 mutation underwent resection of pancreatic cancer. Around three years later, tumor recurrence was detected by MRI and PET-CT confirmed it. She was treated with gemcitabine plus iniparib in clinical trial. Excellent response to therapy was observed and surgery was performed but no residual tumor tissue was detected","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a phase 2 study of 206 recurrent, platinum-sensitive, high-grade ovarian cancer patients, patients with germline or somatic BRCA1 or BRCA2 mutation (n=40) were associated with improved progression free survival (HR 0.27, 95% CI: 0.16-0.44, p<0.0001)  as compared to BRCA1/2 wild-type, loss of heterozygosity low patients (n=71) treated with rucaparib monotherapy; further, BRCA1/2 mutation patients achieved a longer median duration of response (9.2 months, 95% CI: 6.4-12.9, p=0.013 vs. 5.6 months, 95% CI: 4.6-8.5).","In a case report, a 3‐year‐old girl with glioblastoma harboring a probable germline heterozygous BRCA2 Lys3326Ter (K3326*) nonsense variant. After debulking surgery, the patient received standard‐of‐care treatment with radiation and temozolomide. Nine months later the PARP inhibitor olaparib was administered in combination with temozolomide for 16 cycles. This regimen was well tolerated by the patient and serial imaging showed a reduction in tumor size.",null,null,null,null,"The authors show that in the CX-5461 and CX-3543, G-quadruplex stabilizing agents, demonstrate specific toxicity against BRCA deficient breast cancer derived cells and polyclonal patient-derived xenograft models. Xenografts harbored both a germline BRCA and a somatic BRCA mutation leading to disruption of both. The BRCA and NHEJ pathways are required for the repair of CX-5461 and CX-3543-induced DNA damage and failure to do so leads to lethality.","In pancreatic cell lines PL11 (FANCC-deficient) and CAPAN1 (BRCA2-mutated), sensitivity to DNA cross-linking agents was observed compared to FANCC/BRCA2 wildtype cell lines (Su86.86, CFPAC, AsPc1, and MiaPaCa2). Mitomycin C specifically led to regression in 8/11 xenografts of the CAPAN1 cell line compared to 2/9 in the CFPAC (BRCA2 wildtype) cell line.","The authors show that in the CX-5461 and CX-3543, G-quadruplex stabilizing agents, demonstrate specific toxicity against BRCA deficient breast cancer derived cells and polyclonal patient-derived xenograft models. The BRCA and NHE J pathways are required for the repair of CX-5461 and CX-3543-induced DNA damage and failure to do so leads to lethality.","Expression of BRCA1 in 6 mesothelioma cell lines was associated with sensitivity to vinorelbine in functional studies.","In an in vitro study, a SNU-251 cell line expressing BRCA1 W1815X truncating mutation demonstrated increased sensitivity to olaparib treatment with long-term exposure, compared to ovarian cell lines expressing BRCA1 wild-type. Sensitivity was determined by assessing cytotoxicity and doubling time. The authors note that the slow doubling time of SNU-251 cells was compensated for with a 2 week cytotoxicity assay as compared to the 1 week assay used for all other cell lines.",null,null],["Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Resistance","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity","Sensitivity","Sensitivity","Sensitivity","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity/Response","Sensitivity","Sensitivity"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>variant_name<\/th>\n      <th>primary_site<\/th>\n      <th>therapeutic_context<\/th>\n      <th>molecular_profile_name<\/th>\n      <th>evidence_level<\/th>\n      <th>variant_id<\/th>\n      <th>evidence_type<\/th>\n      <th>biomarker_source<\/th>\n      <th>biomarker_source_datestamp<\/th>\n      <th>evidence_id<\/th>\n      <th>variant_origin<\/th>\n      <th>literature_id<\/th>\n      <th>evidence_url<\/th>\n      <th>evidence_description<\/th>\n      <th>clinical_significance<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"buttons":["csv","excel"],"dom":"Bfrtip","columnDefs":[{"className":"dt-right","targets":6},{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"variant_name","targets":1},{"name":"primary_site","targets":2},{"name":"therapeutic_context","targets":3},{"name":"molecular_profile_name","targets":4},{"name":"evidence_level","targets":5},{"name":"variant_id","targets":6},{"name":"evidence_type","targets":7},{"name":"biomarker_source","targets":8},{"name":"biomarker_source_datestamp","targets":9},{"name":"evidence_id","targets":10},{"name":"variant_origin","targets":11},{"name":"literature_id","targets":12},{"name":"evidence_url","targets":13},{"name":"evidence_description","targets":14},{"name":"clinical_significance","targets":15}],"order":[],"autoWidth":false,"orderClasses":false,"responsive":true}},"evals":[],"jsHooks":[]}</script><p><br><br></p>
 </div>
 </div>
 <div class="section level2">
@@ -659,7 +654,7 @@ <h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">#&gt; [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; other attached packages:</span></span>
-<span><span class="co">#&gt; [1] pharmOncoX_1.6.3</span></span>
+<span><span class="co">#&gt; [1] pharmOncoX_1.6.4</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; loaded via a namespace (and not attached):</span></span>
 <span><span class="co">#&gt;  [1] sass_0.4.9        utf8_1.2.4        generics_0.1.3    stringi_1.8.3    </span></span>
diff --git a/authors.html b/authors.html
index 4ef81cd..910f30b 100644
--- a/authors.html
+++ b/authors.html
@@ -15,7 +15,7 @@
     
     <a class="navbar-brand me-2" href="index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -64,12 +64,12 @@ <h2>Authors</h2>
       <h2 id="citation">Citation</h2>
       <p><small class="dont-index">Source: <a href="https://github.com/sigven/pharmOncoX/blob/HEAD/inst/CITATION" class="external-link"><code>inst/CITATION</code></a></small></p>
 
-      <p>Nakken S.  (2024)  pharmOncoX: Targeted and non-targeted anti-cancer drugs and drug regimens.  R package version 1.6.3.  (https://github.com/sigven/pharmOncoX)</p>
+      <p>Nakken S.  (2024)  pharmOncoX: Targeted and non-targeted anti-cancer drugs and drug regimens.  R package version 1.6.4.  (https://github.com/sigven/pharmOncoX)</p>
       <pre>@Manual{,
   title = {pharmOncoX: Targeted and non-targeted anti-cancer drugs and drug regimens},
   author = {Sigve Nakken},
   year = {2024},
-  note = {R package version 1.6.3},
+  note = {R package version 1.6.4},
   url = {https://github.com/sigven/pharmOncoX},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index df362d9..30b0717 100644
--- a/index.html
+++ b/index.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index 9e17613..4ec79dd 100644
--- a/news/index.html
+++ b/news/index.html
@@ -15,7 +15,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -52,6 +52,10 @@
       <small>Source: <a href="https://github.com/sigven/pharmOncoX/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="1.6.4" id="version-164-april-30th-2024">Version 1.6.4 (April 30th 2024)<a class="anchor" aria-label="anchor" href="#version-164-april-30th-2024"></a></h2>
+<ul><li>Improved clinical (tumor site) annotations of fusions from MitelmanDB</li>
+</ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.6.3" id="version-163-april-26th-2024">Version 1.6.3 (April 26th 2024)<a class="anchor" aria-label="anchor" href="#version-163-april-26th-2024"></a></h2>
 <ul><li>Updated CIViC (20240426)</li>
diff --git a/pkgdown.yml b/pkgdown.yml
index 365db67..7e514e1 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   pharmOncoX: pharmOncoX.html
-last_built: 2024-04-26T12:20Z
+last_built: 2024-04-30T12:09Z
 urls:
   reference: https://sigven.github.io/pharmOncoX/reference
   article: https://sigven.github.io/pharmOncoX/articles
diff --git a/reference/get_biomarkers.html b/reference/get_biomarkers.html
index 0272e8e..24030e0 100644
--- a/reference/get_biomarkers.html
+++ b/reference/get_biomarkers.html
@@ -31,7 +31,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_drug_records.html b/reference/get_drug_records.html
index 9decb85..77ab3ed 100644
--- a/reference/get_drug_records.html
+++ b/reference/get_drug_records.html
@@ -15,7 +15,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_drugs.html b/reference/get_drugs.html
index 4b902f3..ac91d01 100644
--- a/reference/get_drugs.html
+++ b/reference/get_drugs.html
@@ -27,7 +27,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_targeted_drugs.html b/reference/get_targeted_drugs.html
index 55fddff..7b428fb 100644
--- a/reference/get_targeted_drugs.html
+++ b/reference/get_targeted_drugs.html
@@ -15,7 +15,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 8007f1c..e6bc977 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -15,7 +15,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/tidyeval.html b/reference/tidyeval.html
index e948a3e..5d924a8 100644
--- a/reference/tidyeval.html
+++ b/reference/tidyeval.html
@@ -15,7 +15,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">pharmOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.6.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index 8258ccd..2dbd081 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/ code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Getting started","text":"","code":"if (!(\"remotes\" %in% installed.packages())) {  install.packages(\"remotes\") } #> Installing package into '/home/runner/work/_temp/Library' #> (as 'lib' is unspecified)  remotes::install_github('sigven/pharmOncoX') #> Using github PAT from envvar GITHUB_PAT. Use `gitcreds::gitcreds_set()` and unset GITHUB_PAT in .Renviron (or elsewhere) if you want to use the more secure git credential store instead. #> Downloading GitHub repo sigven/pharmOncoX@HEAD #> cpp11 (NA -> 0.4.7) [CRAN] #> Installing 1 packages: cpp11 #> Installing package into '/home/runner/work/_temp/Library' #> (as 'lib' is unspecified) #> ── R CMD build ───────────────────────────────────────────────────────────────── #> * checking for file ‘/tmp/Rtmpoc76Ze/remotes295c4c1b57fc/sigven-pharmOncoX-df26048/DESCRIPTION’ ... OK #> * preparing ‘pharmOncoX’: #> * checking DESCRIPTION meta-information ... OK #> * checking for LF line-endings in source and make files and shell scripts #> * checking for empty or unneeded directories #> Omitted ‘LazyData’ from DESCRIPTION #> * building ‘pharmOncoX_1.6.3.tar.gz’ #> Installing package into '/home/runner/work/_temp/Library' #> (as 'lib' is unspecified)  library(pharmOncoX) cache_dir <- tempdir() #cache_dir <-  #  \"/Users/sigven/project_data/packages/package__pharmOncoX/pharmOncoX/data-raw/gd_local\""},{"path":[]},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"targeted-agents","dir":"Articles","previous_headings":"Cancer drug classifications","what":"Targeted agents","title":"Getting started","text":"Plotted key statistics respect drug classification numbers targeted chemotherapy agents found pharmOncoX. Existing drug classifications retrieved ATC, extended manual addition/curation, also establishment multiple novel levels ATC tree, particularly targeted therapies. Note drugs indicated cancer conditions (harvested Open Targets platform) considered numbers plotted .","code":"p_targeted_classifications"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"chemotherapy-agents","dir":"Articles","previous_headings":"Cancer drug classifications","what":"Chemotherapy agents","title":"Getting started","text":"","code":"p_chemo_classifications"},{"path":[]},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-braf-targeted-drugs-list-records-per-indication","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get BRAF-targeted drugs, list records per indication","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,   treatment_category =  c(\"targeted_therapy_classified\",                           \"targeted_therapy_unclassified\"),     drug_target = c('BRAF')) #> INFO  [2024-04-26 12:21:41] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:21:41] Object 'drug_map_name' sucessfully loaded #> INFO  [2024-04-26 12:21:41] Retrieved n = 31451 records #> INFO  [2024-04-26 12:21:42] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:21:42] Object 'drug_map_alias' sucessfully loaded #> INFO  [2024-04-26 12:21:42] Retrieved n = 684962 records #> INFO  [2024-04-26 12:21:42] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:21:42] Object 'drug_map_basic' sucessfully loaded #> INFO  [2024-04-26 12:21:42] Retrieved n = 31487 records #> INFO  [2024-04-26 12:21:42] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:21:42] Object 'drug_map_target' sucessfully loaded #> INFO  [2024-04-26 12:21:42] Retrieved n = 39374 records #> INFO  [2024-04-26 12:21:42] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:21:42] Object 'drug_map_indication' sucessfully loaded #> INFO  [2024-04-26 12:21:42] Retrieved n = 62659 records #> INFO  [2024-04-26 12:21:45] Record set satisfying user-defined criteria: n = 279 #> INFO  [2024-04-26 12:21:45] Collapsing record set - providing output on a 'per_drug_target_indication' resolution #> INFO  [2024-04-26 12:21:45] Final record set: n = 236 records  ## Number of drug records nrow(drugs$records) #> [1] 236  ## Column names of drug records colnames(drugs$records) #>  [1] \"drug_id\"                      \"drug_name\"                    #>  [3] \"drug_type\"                    \"molecule_chembl_id\"           #>  [5] \"drug_action_type\"             \"drug_alias\"                   #>  [7] \"nci_concept_definition\"       \"opentargets\"                  #>  [9] \"drug_cancer_relevance\"        \"inhibition_moa\"               #> [11] \"is_salt\"                      \"is_adc\"                       #> [13] \"drug_blackbox_warning\"        \"nci_t\"                        #> [15] \"target_symbol\"                \"target_entrezgene\"            #> [17] \"target_genename\"              \"target_ensembl_gene_id\"       #> [19] \"target_type\"                  \"drug_max_phase_indication\"    #> [21] \"drug_approved_indication\"     \"drug_frac_cancer_indications\" #> [23] \"drug_approved_noncancer\"      \"drug_n_indications\"           #> [25] \"drug_year_first_approval\"     \"drug_max_ct_phase\"            #> [27] \"disease_efo_id\"               \"disease_efo_label\"            #> [29] \"primary_site\"                 \"drug_clinical_id\"             #> [31] \"drug_clinical_source\"         \"atc_code_level1\"              #> [33] \"atc_level1\"                   \"atc_code_level2\"              #> [35] \"atc_level2\"                   \"atc_code_level3\"              #> [37] \"atc_level3\"                   \"atc_treatment_category\""},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-ras-targeted-drugs-list-per-drug-target","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get RAS-targeted drugs, list per drug target","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category =  c(\"targeted_therapy_classified\"),   drug_action_inhibition = T,   output_resolution = \"drug2target\")$records |>   dplyr::filter(atc_level3 == \"RAS inhibitors\")  drugs <- drugs |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     )  dt_drugtable_ras_inhibitors <- DT::datatable(   drugs,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-mek-inhibitors-list-per-drug-only","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get MEK inhibitors, list per drug only","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category =  c(\"targeted_therapy_classified\"),   drug_action_inhibition = T,   drug_source_opentargets = T,    output_resolution = \"drug\" )$records |>   dplyr::filter(atc_level3 == \"MEK inhibitors\")  drugs <- drugs |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     )  dt_drugtable_mek_inhibitors <- DT::datatable(   drugs,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-immune-checkpoint-inhibitors-list-per-drug-target","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get immune checkpoint inhibitors, list per drug target","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category =  c(\"targeted_therapy_classified\"),   drug_source_opentargets = F,   drug_classified_cancer = T,    output_resolution = \"drug2target\")  drugs$records <- drugs$records |>   dplyr::filter(     (!is.na(atc_level3) &        (atc_level3 == \"PD-1/PDL-1 inhibitors\" |      atc_level3 == \"Other immune checkpoint inhibitors\")   )) |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     ) |>   dplyr::select(     drug_id,     drug_name,     drug_type,     target_symbol,     target_genename,     dplyr::everything()   )  dt_drugtable_ici <- DT::datatable(   drugs$records,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-immune-checkpoint-inhibitors-indicated-for-lung-cancer-conditions-list-per-drug-target-entry","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get immune checkpoint inhibitors indicated for lung cancer conditions, list per drug-target entry","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    output_resolution = \"drug2target\",    treatment_category = c(\"targeted_therapy_classified\"),   drug_source_opentargets = T,   drug_indication_main = \"Lung\")  drugs$records <- drugs$records |>   dplyr::filter(     (!is.na(atc_level3) &        (atc_level3 == \"PD-1/PDL-1 inhibitors\" |      atc_level3 == \"Other immune checkpoint inhibitors\")   )) |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     ) |>   dplyr::select(     drug_id,     drug_name,     drug_type,     target_symbol,     target_genename,     dplyr::everything()   )  dt_drugtable_ici_lung <- DT::datatable(   drugs$records,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-antimetabolite-drugs","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get antimetabolite drugs","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category = c(\"chemo_therapy_classified\"),   output_resolution = \"drug\") #> INFO  [2024-04-26 12:22:04] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:04] Object 'drug_map_name' sucessfully loaded #> INFO  [2024-04-26 12:22:04] Retrieved n = 31451 records #> INFO  [2024-04-26 12:22:05] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:05] Object 'drug_map_alias' sucessfully loaded #> INFO  [2024-04-26 12:22:05] Retrieved n = 684962 records #> INFO  [2024-04-26 12:22:05] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:05] Object 'drug_map_basic' sucessfully loaded #> INFO  [2024-04-26 12:22:05] Retrieved n = 31487 records #> INFO  [2024-04-26 12:22:05] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:05] Object 'drug_map_target' sucessfully loaded #> INFO  [2024-04-26 12:22:05] Retrieved n = 39374 records #> INFO  [2024-04-26 12:22:05] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:05] Object 'drug_map_indication' sucessfully loaded #> INFO  [2024-04-26 12:22:05] Retrieved n = 62659 records #> INFO  [2024-04-26 12:22:08] Record set satisfying user-defined criteria: n = 16503 #> INFO  [2024-04-26 12:22:08] Collapsing record set - providing output on a 'per_drug' resolution #> INFO  [2024-04-26 12:22:08] Final record set: n = 170 records  drugs$records <- drugs$records |>   dplyr::filter(     !is.na(atc_level2) &     stringr::str_detect(       atc_level2, \"ANTIMETABOLITES\"     )   ) |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     )  dt_drugtable_metabolites <- DT::datatable(   drugs$records,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-taxanes","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get taxanes","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category = \"chemo_therapy_classified\",   output_resolution = \"drug\") #> INFO  [2024-04-26 12:22:08] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:08] Object 'drug_map_name' sucessfully loaded #> INFO  [2024-04-26 12:22:08] Retrieved n = 31451 records #> INFO  [2024-04-26 12:22:09] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:09] Object 'drug_map_alias' sucessfully loaded #> INFO  [2024-04-26 12:22:09] Retrieved n = 684962 records #> INFO  [2024-04-26 12:22:09] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:09] Object 'drug_map_basic' sucessfully loaded #> INFO  [2024-04-26 12:22:09] Retrieved n = 31487 records #> INFO  [2024-04-26 12:22:09] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:09] Object 'drug_map_target' sucessfully loaded #> INFO  [2024-04-26 12:22:09] Retrieved n = 39374 records #> INFO  [2024-04-26 12:22:09] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:09] Object 'drug_map_indication' sucessfully loaded #> INFO  [2024-04-26 12:22:09] Retrieved n = 62659 records #> INFO  [2024-04-26 12:22:12] Record set satisfying user-defined criteria: n = 16503 #> INFO  [2024-04-26 12:22:12] Collapsing record set - providing output on a 'per_drug' resolution #> INFO  [2024-04-26 12:22:12] Final record set: n = 170 records  drugs$records <- drugs$records |>   dplyr::filter(     stringr::str_detect(       atc_level3, \"Taxanes\"     )   ) |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     )  dt_drugtable_taxanes <- DT::datatable(   drugs$records,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-platinum-compounds","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get platinum compounds","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category = \"chemo_therapy_classified\",   output_resolution = \"drug\") #> INFO  [2024-04-26 12:22:12] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:12] Object 'drug_map_name' sucessfully loaded #> INFO  [2024-04-26 12:22:12] Retrieved n = 31451 records #> INFO  [2024-04-26 12:22:12] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:12] Object 'drug_map_alias' sucessfully loaded #> INFO  [2024-04-26 12:22:12] Retrieved n = 684962 records #> INFO  [2024-04-26 12:22:13] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:13] Object 'drug_map_basic' sucessfully loaded #> INFO  [2024-04-26 12:22:13] Retrieved n = 31487 records #> INFO  [2024-04-26 12:22:13] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:13] Object 'drug_map_target' sucessfully loaded #> INFO  [2024-04-26 12:22:13] Retrieved n = 39374 records #> INFO  [2024-04-26 12:22:13] Reading from cache_dir = '/tmp/Rtmpoc76Ze', argument force_download = F #> INFO  [2024-04-26 12:22:13] Object 'drug_map_indication' sucessfully loaded #> INFO  [2024-04-26 12:22:13] Retrieved n = 62659 records #> INFO  [2024-04-26 12:22:15] Record set satisfying user-defined criteria: n = 16503 #> INFO  [2024-04-26 12:22:15] Collapsing record set - providing output on a 'per_drug' resolution #> INFO  [2024-04-26 12:22:15] Final record set: n = 170 records  drugs$records <- drugs$records |>   dplyr::filter(     stringr::str_detect(       atc_level3, \"Platinum compounds\"     )   ) |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     )  dt_drugtable_platins <- DT::datatable(   drugs$records,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":[]},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"reported-associations-between-brca12-alterations-and-drug-sensitivity","dir":"Articles","previous_headings":"Retrieval of biomarkers","what":"Reported associations between BRCA1/2 alterations and drug sensitivity","title":"Getting started","text":"Get evidence CIViC CGI cancer drug sensitivity BRCA1/2 alterations (somatically (tumor) inherited/germline)","code":"biomarkers <- get_biomarkers(   cache_dir = cache_dir) #> INFO  [2024-04-26 12:22:15] Downloading remote dataset from Google Drive to cache_dir #> INFO  [2024-04-26 12:22:22] Reading from cache_dir = ' (/tmp/Rtmpoc76Ze'), argument force_download = F #> INFO  [2024-04-26 12:22:22] Object 'biomarkers' sucessfully loaded #> INFO  [2024-04-26 12:22:22] md5 checksum is valid: 28ca0e6165547bf46b102436344a43a1  brca1_biomarkers <- list() for(source in c('civic','cgi')){   brca1_biomarkers[[source]] <-      biomarkers$data[[source]]$variant |>      dplyr::filter(       !is.na(symbol) & (symbol == \"BRCA1\" | symbol == \"BRCA2\")) |>     dplyr::group_by(variant_id, variant_name_primary, variant_consequence) |>     dplyr::summarise(       variant_alias = paste(variant_alias, collapse=\", \"),        .groups = \"drop\") |>      dplyr::inner_join(       biomarkers$data[[source]]$clinical, by = \"variant_id\") |>     dplyr::select(       variant_id, variant_name_primary, therapeutic_context,       evidence_type, evidence_level,        biomarker_source, biomarker_source_datestamp,       molecular_profile_name, evidence_id, variant_origin,       primary_site, evidence_id, source_id,       evidence_url,        evidence_description,        clinical_significance) |>      dplyr::distinct() |>      dplyr::rename(literature_id = source_id,                   variant_name = variant_name_primary) |>     dplyr::filter(evidence_type == \"Predictive\") |>     dplyr::select(       variant_name,        primary_site,       therapeutic_context,       molecular_profile_name,        evidence_level,       dplyr::everything()     ) }  brca1_biomarkers_all <-    dplyr::bind_rows(brca1_biomarkers[['civic']],                    brca1_biomarkers[['cgi']]) |>     dplyr::arrange(evidence_level)     dt_brca1_biomarkers <- DT::datatable(   brca1_biomarkers_all,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Getting started","text":"","code":"# set eval = FALSE if you don't want this info (useful for reproducibility)  # to appear sessionInfo() #> R version 4.4.0 (2024-04-24) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] pharmOncoX_1.6.3 #>  #> loaded via a namespace (and not attached): #>  [1] sass_0.4.9        utf8_1.2.4        generics_0.1.3    stringi_1.8.3     #>  [5] digest_0.6.35     magrittr_2.0.3    evaluate_0.23     grid_4.4.0        #>  [9] fastmap_1.1.1     jsonlite_1.8.8    processx_3.8.4    pkgbuild_1.4.4    #> [13] googledrive_2.1.1 ps_1.7.6          httr_1.4.7        purrr_1.0.2       #> [17] fansi_1.0.6       crosstalk_1.2.1   scales_1.3.0      textshaping_0.3.7 #> [21] jquerylib_0.1.4   cli_3.6.2         rlang_1.1.3       crayon_1.5.2      #> [25] munsell_0.5.1     remotes_2.5.0     withr_3.0.0       cachem_1.0.8      #> [29] yaml_2.3.8        tools_4.4.0       gargle_1.5.2      memoise_2.0.1     #> [33] dplyr_1.1.4       colorspace_2.1-0  ggplot2_3.5.1     DT_0.33           #> [37] curl_5.2.1        assertthat_0.2.1  vctrs_0.6.5       R6_2.5.1          #> [41] lifecycle_1.0.4   stringr_1.5.1     fs_1.6.4          htmlwidgets_1.6.4 #> [45] ragg_1.3.0        pkgconfig_2.0.3   desc_1.4.3        callr_3.7.6       #> [49] gtable_0.3.5      pkgdown_2.0.9     pillar_1.9.0      bslib_0.7.0       #> [53] glue_1.7.0        lgr_0.4.4         systemfonts_1.0.6 highr_0.10        #> [57] xfun_0.43         tibble_3.2.1      tidyselect_1.2.1  knitr_1.46        #> [61] farver_2.1.1      htmltools_0.5.8.1 rmarkdown_2.26    compiler_4.4.0"},{"path":[]},{"path":"https://sigven.github.io/pharmOncoX/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sigve Nakken. Author, maintainer.","code":""},{"path":"https://sigven.github.io/pharmOncoX/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Nakken S.  (2024)  pharmOncoX: Targeted non-targeted anti-cancer drugs drug regimens.  R package version 1.6.3.  (https://github.com/sigven/pharmOncoX)","code":"@Manual{,   title = {pharmOncoX: Targeted and non-targeted anti-cancer drugs and drug regimens},   author = {Sigve Nakken},   year = {2024},   note = {R package version 1.6.3},   url = {https://github.com/sigven/pharmOncoX}, }"},{"path":"https://sigven.github.io/pharmOncoX/index.html","id":"pharmoncox-","dir":"","previous_headings":"","what":"Molecularly targeted cancer drugs and biomarkers","title":"Molecularly targeted cancer drugs and biomarkers","text":"pharmOncoX provides access targeted non-targeted cancer drugs, including comprehensive annotations per target, drug mechanism--action, approval dates, clinical trial phases various indications etc. data largely based drug-target-indication associations provided Open Targets Platform (Ochoa et al., Nucleic Acids Res., 2021). Associations retrieved Open Targets Platform integrated cancer-relevant indications/conditions (provided sigven/phenOncoX), allowing user retrieve drugs indicated main tumor types (e.g. Lung, Colon/Rectum etc.) Drug-target associations Open Targets Platform furthermore integrated appended drug information NCI Thesaurus, showing also non-targeted cancer drugs (chemotherapeutic agents etc.), various drug regimens. pharmOncoX provides anti-cancer drug classification existing entries Anatomical Therapeutic Chemical (ATC) Classification System, extended significantly manual curation, also establishing novel drug categories presently missing ATC classificiation tree (examples include AURK inhibitors, MET inhibitors, BET inhibitors, AKT inhibitors, PLK inhibitors, IAP inhibitors etc.) enabling filtering drugs according main mechanisms action. Currently (late February 2024), pharmOncoX built upon following releases external databases: Open Targets Platform (2023.12) ChEMBL (v33) NCI Thesaurus (24.01e)","code":""},{"path":"https://sigven.github.io/pharmOncoX/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Molecularly targeted cancer drugs and biomarkers","text":"Installation instructions Usage examples","code":""},{"path":"https://sigven.github.io/pharmOncoX/index.html","id":"contact","dir":"","previous_headings":"","what":"Contact","title":"Molecularly targeted cancer drugs and biomarkers","text":"sigven ifi.uio.","code":""},{"path":"https://sigven.github.io/pharmOncoX/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Molecularly targeted cancer drugs and biomarkers","text":"Please note project released Contributor Code Conduct. participating project agree abide terms.","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_biomarkers.html","id":null,"dir":"Reference","previous_headings":"","what":"Get curated cancer biomarker datasets — get_biomarkers","title":"Get curated cancer biomarker datasets — get_biomarkers","text":"Downloads preprocessed datasets local cache directory returns curated set genomic biomarkers multiple sources (CIViC, CGI, MitelmanDB) dataset comes list object, three elements: metadata - data frame metadata regarding drug resources used data - list four elements ('civic','cgi','mitelmandb','custom_fusions') fpath - path cache file","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_biomarkers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get curated cancer biomarker datasets — get_biomarkers","text":"","code":"get_biomarkers(cache_dir = NA, force_download = F)"},{"path":"https://sigven.github.io/pharmOncoX/reference/get_biomarkers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get curated cancer biomarker datasets — get_biomarkers","text":"cache_dir Local directory data download force_download Logical indicating local cache force downloaded (.e. set TRUE re-download even data exists cache)","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_biomarkers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get curated cancer biomarker datasets — get_biomarkers","text":"entry source-specific (e.g. 'civic') entry data list contains list three data frames: variant - list biomarker variants, extensively populated according variant aliases (identifer - column variant_id) clinical - cross-references variants recorded variant data frame clinical evidence items (identifier - column evidence_id) underlying literature evidence (identifier - column source_id) literature - lists literature source_id's listed clinical data frame","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drug_records.html","id":null,"dir":"Reference","previous_headings":"","what":"Function that retrieves pharmOncoX data from Google Drive — get_drug_records","title":"Function that retrieves pharmOncoX data from Google Drive — get_drug_records","text":"Function retrieves pharmOncoX data Google Drive","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drug_records.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that retrieves pharmOncoX data from Google Drive — get_drug_records","text":"","code":"get_drug_records(cache_dir = NA, force_download = F)"},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drug_records.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that retrieves pharmOncoX data from Google Drive — get_drug_records","text":"cache_dir Local directory data download force_download Logical indicating local cache force downloaded (.e. set TRUE re-download even data exists cache)","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drugs.html","id":null,"dir":"Reference","previous_headings":"","what":"Get antineoplastic drugs and drug regimens — get_drugs","title":"Get antineoplastic drugs and drug regimens — get_drugs","text":"Downloads preprocessed datasets local cache directory returns selected set drugs based various criteria set user. dataset comes list object, two elements: metadata - data frame metadata regarding drug resources used records - data frame drug records","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drugs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get antineoplastic drugs and drug regimens — get_drugs","text":"","code":"get_drugs(   cache_dir = NA,   force_download = FALSE,   exclude_salt_forms = TRUE,   exclude_adc = FALSE,   treatment_category = c(\"targeted_therapy_classified\", \"targeted_therapy_unclassified\",     \"chemo_therapy_classified\", \"hormone_therapy_classified\",     \"immuno_suppressants_classified\", \"other\"),   drug_is_approved = FALSE,   drug_target = NULL,   drug_action_type = NULL,   drug_indication_main = NULL,   drug_source_opentargets = FALSE,   drug_cancer_indication = TRUE,   drug_classified_cancer = TRUE,   drug_has_blackbox_warning = FALSE,   drug_approval_year = 1939,   drug_minimum_phase_any_indication = 0,   output_resolution = \"drug2target2indication\",   drug_action_inhibition = F )"},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drugs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get antineoplastic drugs and drug regimens — get_drugs","text":"cache_dir local cache directory data retrieval force_download force download data remote repository even data exists cache exclude_salt_forms exclude salt forms drugs exclude_adc exclude antibody-drug conjugates (ADCs) treatment_category main treatment category, classified according ATC ('targeted_therapy_classified', 'targeted_therapy_unclassified','chemo_therapy_classified','hormone_therapy_classified', 'immuno_suppressants_classified','') drug_is_approved logical indicating resulting drug records contain approved drugs drug_target character vector drug targets (gene symbols) drug records included results drug_action_type character vector drug action types include drug record list - possible values \"INHIBITOR\",\"AGONIST\",\"MODULATOR\",\"ANTAGONIST\", \"BLOCKER\",\"ACTIVATOR\",\"BINDING AGENT\",\"OPENER\", \"STABILISER\",\"CROSS-LINKING AGENT\",DISRUPTING AGENT\",\"\" drug_indication_main character vector main tumor types drug(s) indicated. Possible values: \"Adrenal Gland\",\"Biliary Tract\", \"Bladder/Urinary Tract\",\"Bone\",\"Breast\",\"Cervix\",\"CNS/Brain\", \"Colon/Rectum\",\"Esophagus/Stomach\",\"Eye\",\"Head Neck\",\"Kidney\", \"Liver\",\"Lung\",\"Lymphoid\",\"Myeloid\",\"Ovary/Fallopian Tube\", \"Pancreas\",\"Penis\",\"Peripheral Nervous System\",\"Peritoneum\", \"Pleura\",\"Prostate\",\"Skin\",\"Soft Tissue\",\"Testis\",\"Thymus\", \"Thyroid\",\"Uterus\",\"Vulva/Vagina\" drug_source_opentargets logical indicating resulting drug records contain drug records Open Targets Platform/ChEMBL drug_cancer_indication logical indicating resulting drug records indicated cancer conditions (approved conditions, found clinical trials etc.) drug_classified_cancer logical indicating resulting drug records classified \"L\" class ATC ( \"ANTINEOPLASTIC IMMUNOMODULATING AGENTS\") drug_has_blackbox_warning logical indicating resulting drug records contain drugs black box warnings drug_approval_year include records drugs approved later date (year) drug_minimum_phase_any_indication include drug records clinical phase (indication) greater equal phase output_resolution dictate output record resolution ('drug','drug2target','drug2target2indication') drug_action_inhibition logical indicating return drug records inhibitory mechanism--action","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drugs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get antineoplastic drugs and drug regimens — get_drugs","text":"records data frame contains following columns (selected columns shown based value output_resolution) drug_id - drug identifier (pharmaOncoX) drug_name - primary drug name (upper case, NCI Thesaurus) drug_type - type drug molecule (Antibody, small molecule etc) molecule_chembl_id - ChEMBL compound identifier drug_action_type - main action elicited drug (antagonist, inhibitor, stabiliser etc) drug_alias - collection unambiguous drug aliases (separated '|') nci_concept_definition - detailed description drug mechanism--action (NCI Thesaurus) opentargets - logical - drug found Open Targets Platform resource is_salt - logical - drug record represents salt form (excluded default) is_adc - logical - drug record represents antibody-drug conjugate (ADC - excluded default) drug_blacbox_warning - logical indicating drug blackbox warning nci_t - NCI thesaurus identifier target_symbol - gene symbol drug target target_entrezgene - Entrez gene identifier drug target target_genename - gene name/description drug target target_ensembl_gene_id - Ensembl gene identifier drug target target_type - type drug target (single protein, protein family etc.) drug_max_phase_indication - maximum clinical phase drug (given indication) drug_approved_indication - logical indicating drug approved indication drug_frac_cancer_indications - fraction drug indications cancers drug_approved_noncancer - logical indicating drug approved non-cancer disease drug_n_indications - number indications given drug (approved indications, clinical trials etc) drug_year_first_approval - year drug first approved drug_max_ct_phase - maximum clinical phase drug (indication) disease_efo_id - EFO (Experimental Factor Ontology) identifier drug indication disease_efo_label - EFO (Experimental Factor Ontology) label drug indication primary_site - primary tumor site/type (obtained https://github.com/sigven/oncoPhenoMap) drug_clinical_id - drug clinical identifier (clinicaltrials.gov, DailyMed, FDA etc.) drug_clinical_source - underlying source drug entry (DailyMed, clinicaltrials.gov, FDA etc.) atc_code_level1 - drug identifier ATC (level 1) atc_level1 - drug label ATC (level 1) atc_code_level1 - drug identifier ATC (level 2) atc_level2 - drug label ATC (level 2) atc_code_level3 - drug identifier ATC (level 3) atc_level3 - drug label ATC (level 3) atc_treatment_category - treatment category (targeted/chemo/hormone, cancer/etc)","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_targeted_drugs.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to get on-label/off-label drugs (not complete) — get_targeted_drugs","title":"Utility function to get on-label/off-label drugs (not complete) — get_targeted_drugs","text":"Utility function get -label/-label drugs (complete)","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_targeted_drugs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to get on-label/off-label drugs (not complete) — get_targeted_drugs","text":"","code":"get_targeted_drugs(cache_dir = NA)"},{"path":"https://sigven.github.io/pharmOncoX/reference/get_targeted_drugs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to get on-label/off-label drugs (not complete) — get_targeted_drugs","text":"cache_dir Local cache directory","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/tidyeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy eval helpers — tidyeval","title":"Tidy eval helpers — tidyeval","text":"https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-163-april-26th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.6.3 (April 26th 2024)","title":"Version 1.6.3 (April 26th 2024)","text":"Updated CIViC (20240426)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-162-april-12th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.6.2 (April 12th 2024)","title":"Version 1.6.2 (April 12th 2024)","text":"Updated NCI Thesaurus (24.03d)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-161-march-26th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.6.1 (March 26th 2024)","title":"Version 1.6.1 (March 26th 2024)","text":"Open Targets Platform update (v2024.03)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-160-march-9th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.6.0 (March 9th 2024)","title":"Version 1.6.0 (March 9th 2024)","text":"CIViC/Mitelmandb updates","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-159-february-29th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.5.9 (February 29th 2024)","title":"Version 1.5.9 (February 29th 2024)","text":"Updated CIViC","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-158-february-6th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.5.8 (February 6th 2024)","title":"Version 1.5.8 (February 6th 2024)","text":"NCI Thesaurus 24.01e","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-157-february-3rd-2024","dir":"Changelog","previous_headings":"","what":"Version 1.5.7 (February 3rd 2024)","title":"Version 1.5.7 (February 3rd 2024)","text":"Fixed buggy alias PubChem","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-156-january-31st-2024","dir":"Changelog","previous_headings":"","what":"Version 1.5.6 (January 31st 2024)","title":"Version 1.5.6 (January 31st 2024)","text":"Refine possible values treatment_category argument get_drugs() function Fix anti-androgen classification Fixed bug alias type notation copy numbers expression biomarkers Filter noise rank output helper function get_targeted_drugs Include variant primary name biomarker variants","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-150-january-25th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.5.0 (January 25th 2024)","title":"Version 1.5.0 (January 25th 2024)","text":"Considerable improvement drug classifications (output column atc_level3), considering targeted agents chemotherapy argument drug_targeted_agent renamed treatment_category helper function get_on_off_label_drugs renamed get_targeted_drugs","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-1410-january-17th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.4.10 (January 17th 2024)","title":"Version 1.4.10 (January 17th 2024)","text":"Updated NCI Thesaurus (23.12d) Updated CIViC data (20240114) Revised manual drug classification (building upon ATC)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-148-december-12th-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.8 (December 12th 2023)","title":"Version 1.4.8 (December 12th 2023)","text":"Updated NCI Thesaurus - 23.11d Updated CIViC data (20231212)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-148-november-30th-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.8 (November 30th 2023)","title":"Version 1.4.8 (November 30th 2023)","text":"Updated OTP (v2023.12) Updated Mitelman database (20231016)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-147-november-3rd-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.7 (November 3rd 2023)","title":"Version 1.4.7 (November 3rd 2023)","text":"Fixed corrupt biomarker literature data frame","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-146-october-18th-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.6 (October 18th 2023)","title":"Version 1.4.6 (October 18th 2023)","text":"Fixed metadata Fixed -dated version descriptions (GH site) exclude compounds missing drug action type (platins etc.)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-145-october-6th-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.5 (October 6th 2023)","title":"Version 1.4.5 (October 6th 2023)","text":"Updated NCI Thesaurus - 23.09d Updated CIViC data Added drug class (ATC) get_on_off_label_drugs()","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-144-september-1st-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.4 (September 1st 2023)","title":"Version 1.4.4 (September 1st 2023)","text":"Updated NCI Thesaurus - 23.08d Updated CIViC data Updated Mitelman database (20230803) get_biomarkers() now exported main function","code":""}]
+[{"path":[]},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://sigven.github.io/pharmOncoX/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/ code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Getting started","text":"","code":"if (!(\"remotes\" %in% installed.packages())) {  install.packages(\"remotes\") }  remotes::install_github('sigven/pharmOncoX') #> Using github PAT from envvar GITHUB_PAT. Use `gitcreds::gitcreds_set()` and unset GITHUB_PAT in .Renviron (or elsewhere) if you want to use the more secure git credential store instead. #> Downloading GitHub repo sigven/pharmOncoX@HEAD #>  #> ── R CMD build ───────────────────────────────────────────────────────────────── #> * checking for file ‘/tmp/RtmpuP6uPL/remotes18615796bfc/sigven-pharmOncoX-c9d5fff/DESCRIPTION’ ... OK #> * preparing ‘pharmOncoX’: #> * checking DESCRIPTION meta-information ... OK #> * checking for LF line-endings in source and make files and shell scripts #> * checking for empty or unneeded directories #> Omitted ‘LazyData’ from DESCRIPTION #> * building ‘pharmOncoX_1.6.4.tar.gz’ #> Installing package into '/home/runner/work/_temp/Library' #> (as 'lib' is unspecified)  library(pharmOncoX) cache_dir <- tempdir() #cache_dir <-  #  \"/Users/sigven/project_data/packages/package__pharmOncoX/pharmOncoX/data-raw/gd_local\""},{"path":[]},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"targeted-agents","dir":"Articles","previous_headings":"Cancer drug classifications","what":"Targeted agents","title":"Getting started","text":"Plotted key statistics respect drug classification numbers targeted chemotherapy agents found pharmOncoX. Existing drug classifications retrieved ATC, extended manual addition/curation, also establishment multiple novel levels ATC tree, particularly targeted therapies. Note drugs indicated cancer conditions (harvested Open Targets platform) considered numbers plotted .","code":"p_targeted_classifications"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"chemotherapy-agents","dir":"Articles","previous_headings":"Cancer drug classifications","what":"Chemotherapy agents","title":"Getting started","text":"","code":"p_chemo_classifications"},{"path":[]},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-braf-targeted-drugs-list-records-per-indication","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get BRAF-targeted drugs, list records per indication","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,   treatment_category =  c(\"targeted_therapy_classified\",                           \"targeted_therapy_unclassified\"),     drug_target = c('BRAF')) #> INFO  [2024-04-30 12:10:10] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:10] Object 'drug_map_name' sucessfully loaded #> INFO  [2024-04-30 12:10:10] Retrieved n = 31451 records #> INFO  [2024-04-30 12:10:10] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:10] Object 'drug_map_alias' sucessfully loaded #> INFO  [2024-04-30 12:10:10] Retrieved n = 687338 records #> INFO  [2024-04-30 12:10:11] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:11] Object 'drug_map_basic' sucessfully loaded #> INFO  [2024-04-30 12:10:11] Retrieved n = 31487 records #> INFO  [2024-04-30 12:10:11] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:11] Object 'drug_map_target' sucessfully loaded #> INFO  [2024-04-30 12:10:11] Retrieved n = 39374 records #> INFO  [2024-04-30 12:10:11] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:11] Object 'drug_map_indication' sucessfully loaded #> INFO  [2024-04-30 12:10:11] Retrieved n = 62659 records #> INFO  [2024-04-30 12:10:13] Record set satisfying user-defined criteria: n = 279 #> INFO  [2024-04-30 12:10:13] Collapsing record set - providing output on a 'per_drug_target_indication' resolution #> INFO  [2024-04-30 12:10:13] Final record set: n = 236 records  ## Number of drug records nrow(drugs$records) #> [1] 236  ## Column names of drug records colnames(drugs$records) #>  [1] \"drug_id\"                      \"drug_name\"                    #>  [3] \"drug_type\"                    \"molecule_chembl_id\"           #>  [5] \"drug_action_type\"             \"drug_alias\"                   #>  [7] \"nci_concept_definition\"       \"opentargets\"                  #>  [9] \"drug_cancer_relevance\"        \"inhibition_moa\"               #> [11] \"is_salt\"                      \"is_adc\"                       #> [13] \"drug_blackbox_warning\"        \"nci_t\"                        #> [15] \"target_symbol\"                \"target_entrezgene\"            #> [17] \"target_genename\"              \"target_ensembl_gene_id\"       #> [19] \"target_type\"                  \"drug_max_phase_indication\"    #> [21] \"drug_approved_indication\"     \"drug_frac_cancer_indications\" #> [23] \"drug_approved_noncancer\"      \"drug_n_indications\"           #> [25] \"drug_year_first_approval\"     \"drug_max_ct_phase\"            #> [27] \"disease_efo_id\"               \"disease_efo_label\"            #> [29] \"primary_site\"                 \"drug_clinical_id\"             #> [31] \"drug_clinical_source\"         \"atc_code_level1\"              #> [33] \"atc_level1\"                   \"atc_code_level2\"              #> [35] \"atc_level2\"                   \"atc_code_level3\"              #> [37] \"atc_level3\"                   \"atc_treatment_category\""},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-ras-targeted-drugs-list-per-drug-target","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get RAS-targeted drugs, list per drug target","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category =  c(\"targeted_therapy_classified\"),   drug_action_inhibition = T,   output_resolution = \"drug2target\")$records |>   dplyr::filter(atc_level3 == \"RAS inhibitors\")  drugs <- drugs |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     )  dt_drugtable_ras_inhibitors <- DT::datatable(   drugs,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-mek-inhibitors-list-per-drug-only","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get MEK inhibitors, list per drug only","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category =  c(\"targeted_therapy_classified\"),   drug_action_inhibition = T,   drug_source_opentargets = T,    output_resolution = \"drug\" )$records |>   dplyr::filter(atc_level3 == \"MEK inhibitors\")  drugs <- drugs |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     )  dt_drugtable_mek_inhibitors <- DT::datatable(   drugs,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-immune-checkpoint-inhibitors-list-per-drug-target","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get immune checkpoint inhibitors, list per drug target","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category =  c(\"targeted_therapy_classified\"),   drug_source_opentargets = F,   drug_classified_cancer = T,    output_resolution = \"drug2target\")  drugs$records <- drugs$records |>   dplyr::filter(     (!is.na(atc_level3) &        (atc_level3 == \"PD-1/PDL-1 inhibitors\" |      atc_level3 == \"Other immune checkpoint inhibitors\")   )) |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     ) |>   dplyr::select(     drug_id,     drug_name,     drug_type,     target_symbol,     target_genename,     dplyr::everything()   )  dt_drugtable_ici <- DT::datatable(   drugs$records,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-immune-checkpoint-inhibitors-indicated-for-lung-cancer-conditions-list-per-drug-target-entry","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get immune checkpoint inhibitors indicated for lung cancer conditions, list per drug-target entry","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    output_resolution = \"drug2target\",    treatment_category = c(\"targeted_therapy_classified\"),   drug_source_opentargets = T,   drug_indication_main = \"Lung\")  drugs$records <- drugs$records |>   dplyr::filter(     (!is.na(atc_level3) &        (atc_level3 == \"PD-1/PDL-1 inhibitors\" |      atc_level3 == \"Other immune checkpoint inhibitors\")   )) |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     ) |>   dplyr::select(     drug_id,     drug_name,     drug_type,     target_symbol,     target_genename,     dplyr::everything()   )  dt_drugtable_ici_lung <- DT::datatable(   drugs$records,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-antimetabolite-drugs","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get antimetabolite drugs","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category = c(\"chemo_therapy_classified\"),   output_resolution = \"drug\") #> INFO  [2024-04-30 12:10:32] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:32] Object 'drug_map_name' sucessfully loaded #> INFO  [2024-04-30 12:10:32] Retrieved n = 31451 records #> INFO  [2024-04-30 12:10:33] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:33] Object 'drug_map_alias' sucessfully loaded #> INFO  [2024-04-30 12:10:33] Retrieved n = 687338 records #> INFO  [2024-04-30 12:10:33] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:33] Object 'drug_map_basic' sucessfully loaded #> INFO  [2024-04-30 12:10:33] Retrieved n = 31487 records #> INFO  [2024-04-30 12:10:33] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:33] Object 'drug_map_target' sucessfully loaded #> INFO  [2024-04-30 12:10:33] Retrieved n = 39374 records #> INFO  [2024-04-30 12:10:33] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:33] Object 'drug_map_indication' sucessfully loaded #> INFO  [2024-04-30 12:10:33] Retrieved n = 62659 records #> INFO  [2024-04-30 12:10:36] Record set satisfying user-defined criteria: n = 16503 #> INFO  [2024-04-30 12:10:36] Collapsing record set - providing output on a 'per_drug' resolution #> INFO  [2024-04-30 12:10:36] Final record set: n = 170 records  drugs$records <- drugs$records |>   dplyr::filter(     !is.na(atc_level2) &     stringr::str_detect(       atc_level2, \"ANTIMETABOLITES\"     )   ) |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     )  dt_drugtable_metabolites <- DT::datatable(   drugs$records,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-taxanes","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get taxanes","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category = \"chemo_therapy_classified\",   output_resolution = \"drug\") #> INFO  [2024-04-30 12:10:36] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:36] Object 'drug_map_name' sucessfully loaded #> INFO  [2024-04-30 12:10:36] Retrieved n = 31451 records #> INFO  [2024-04-30 12:10:36] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:36] Object 'drug_map_alias' sucessfully loaded #> INFO  [2024-04-30 12:10:36] Retrieved n = 687338 records #> INFO  [2024-04-30 12:10:37] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:37] Object 'drug_map_basic' sucessfully loaded #> INFO  [2024-04-30 12:10:37] Retrieved n = 31487 records #> INFO  [2024-04-30 12:10:37] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:37] Object 'drug_map_target' sucessfully loaded #> INFO  [2024-04-30 12:10:37] Retrieved n = 39374 records #> INFO  [2024-04-30 12:10:37] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:37] Object 'drug_map_indication' sucessfully loaded #> INFO  [2024-04-30 12:10:37] Retrieved n = 62659 records #> INFO  [2024-04-30 12:10:39] Record set satisfying user-defined criteria: n = 16503 #> INFO  [2024-04-30 12:10:39] Collapsing record set - providing output on a 'per_drug' resolution #> INFO  [2024-04-30 12:10:39] Final record set: n = 170 records  drugs$records <- drugs$records |>   dplyr::filter(     stringr::str_detect(       atc_level3, \"Taxanes\"     )   ) |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     )  dt_drugtable_taxanes <- DT::datatable(   drugs$records,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"get-platinum-compounds","dir":"Articles","previous_headings":"Retrieval of drugs - examples","what":"Get platinum compounds","title":"Getting started","text":"","code":"drugs <- get_drugs(   cache_dir = cache_dir,    treatment_category = \"chemo_therapy_classified\",   output_resolution = \"drug\") #> INFO  [2024-04-30 12:10:40] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:40] Object 'drug_map_name' sucessfully loaded #> INFO  [2024-04-30 12:10:40] Retrieved n = 31451 records #> INFO  [2024-04-30 12:10:40] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:40] Object 'drug_map_alias' sucessfully loaded #> INFO  [2024-04-30 12:10:40] Retrieved n = 687338 records #> INFO  [2024-04-30 12:10:40] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:40] Object 'drug_map_basic' sucessfully loaded #> INFO  [2024-04-30 12:10:40] Retrieved n = 31487 records #> INFO  [2024-04-30 12:10:40] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:40] Object 'drug_map_target' sucessfully loaded #> INFO  [2024-04-30 12:10:40] Retrieved n = 39374 records #> INFO  [2024-04-30 12:10:40] Reading from cache_dir = '/tmp/RtmpuP6uPL', argument force_download = F #> INFO  [2024-04-30 12:10:40] Object 'drug_map_indication' sucessfully loaded #> INFO  [2024-04-30 12:10:40] Retrieved n = 62659 records #> INFO  [2024-04-30 12:10:43] Record set satisfying user-defined criteria: n = 16503 #> INFO  [2024-04-30 12:10:43] Collapsing record set - providing output on a 'per_drug' resolution #> INFO  [2024-04-30 12:10:43] Final record set: n = 170 records  drugs$records <- drugs$records |>   dplyr::filter(     stringr::str_detect(       atc_level3, \"Platinum compounds\"     )   ) |>   dplyr::select(     -c(\"drug_alias\",        \"disease_main_group\",        \"drug_clinical_id\")) |>   dplyr::mutate(     disease_indication = stringr::str_replace_all(       disease_indication, \"\\\\|\",\", \")     )  dt_drugtable_platins <- DT::datatable(   drugs$records,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":[]},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"reported-associations-between-brca12-alterations-and-drug-sensitivity","dir":"Articles","previous_headings":"Retrieval of biomarkers","what":"Reported associations between BRCA1/2 alterations and drug sensitivity","title":"Getting started","text":"Get evidence CIViC CGI cancer drug sensitivity BRCA1/2 alterations (somatically (tumor) inherited/germline)","code":"biomarkers <- get_biomarkers(   cache_dir = cache_dir) #> INFO  [2024-04-30 12:10:43] Downloading remote dataset from Google Drive to cache_dir #> INFO  [2024-04-30 12:10:46] Reading from cache_dir = ' (/tmp/RtmpuP6uPL'), argument force_download = F #> INFO  [2024-04-30 12:10:46] Object 'biomarkers' sucessfully loaded #> INFO  [2024-04-30 12:10:46] md5 checksum is valid: 5abd5dce7bf710c3106906a18f81f30d  brca1_biomarkers <- list() for(source in c('civic','cgi')){   brca1_biomarkers[[source]] <-      biomarkers$data[[source]]$variant |>      dplyr::filter(       !is.na(symbol) & (symbol == \"BRCA1\" | symbol == \"BRCA2\")) |>     dplyr::group_by(variant_id, variant_name_primary, variant_consequence) |>     dplyr::summarise(       variant_alias = paste(variant_alias, collapse=\", \"),        .groups = \"drop\") |>      dplyr::inner_join(       biomarkers$data[[source]]$clinical, by = \"variant_id\") |>     dplyr::select(       variant_id, variant_name_primary, therapeutic_context,       evidence_type, evidence_level,        biomarker_source, biomarker_source_datestamp,       molecular_profile_name, evidence_id, variant_origin,       primary_site, evidence_id, source_id,       evidence_url,        evidence_description,        clinical_significance) |>      dplyr::distinct() |>      dplyr::rename(literature_id = source_id,                   variant_name = variant_name_primary) |>     dplyr::filter(evidence_type == \"Predictive\") |>     dplyr::select(       variant_name,        primary_site,       therapeutic_context,       molecular_profile_name,        evidence_level,       dplyr::everything()     ) }  brca1_biomarkers_all <-    dplyr::bind_rows(brca1_biomarkers[['civic']],                    brca1_biomarkers[['cgi']]) |>     dplyr::arrange(evidence_level)     dt_brca1_biomarkers <- DT::datatable(   brca1_biomarkers_all,   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\") )"},{"path":"https://sigven.github.io/pharmOncoX/articles/pharmOncoX.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Getting started","text":"","code":"# set eval = FALSE if you don't want this info (useful for reproducibility)  # to appear sessionInfo() #> R version 4.4.0 (2024-04-24) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] pharmOncoX_1.6.4 #>  #> loaded via a namespace (and not attached): #>  [1] sass_0.4.9        utf8_1.2.4        generics_0.1.3    stringi_1.8.3     #>  [5] digest_0.6.35     magrittr_2.0.3    evaluate_0.23     grid_4.4.0        #>  [9] fastmap_1.1.1     jsonlite_1.8.8    processx_3.8.4    pkgbuild_1.4.4    #> [13] googledrive_2.1.1 ps_1.7.6          httr_1.4.7        purrr_1.0.2       #> [17] fansi_1.0.6       crosstalk_1.2.1   scales_1.3.0      textshaping_0.3.7 #> [21] jquerylib_0.1.4   cli_3.6.2         rlang_1.1.3       crayon_1.5.2      #> [25] munsell_0.5.1     remotes_2.5.0     withr_3.0.0       cachem_1.0.8      #> [29] yaml_2.3.8        tools_4.4.0       gargle_1.5.2      memoise_2.0.1     #> [33] dplyr_1.1.4       colorspace_2.1-0  ggplot2_3.5.1     DT_0.33           #> [37] curl_5.2.1        assertthat_0.2.1  vctrs_0.6.5       R6_2.5.1          #> [41] lifecycle_1.0.4   stringr_1.5.1     fs_1.6.4          htmlwidgets_1.6.4 #> [45] ragg_1.3.0        pkgconfig_2.0.3   desc_1.4.3        callr_3.7.6       #> [49] gtable_0.3.5      pkgdown_2.0.9     pillar_1.9.0      bslib_0.7.0       #> [53] glue_1.7.0        lgr_0.4.4         systemfonts_1.0.6 highr_0.10        #> [57] xfun_0.43         tibble_3.2.1      tidyselect_1.2.1  knitr_1.46        #> [61] farver_2.1.1      htmltools_0.5.8.1 rmarkdown_2.26    compiler_4.4.0"},{"path":[]},{"path":"https://sigven.github.io/pharmOncoX/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sigve Nakken. Author, maintainer.","code":""},{"path":"https://sigven.github.io/pharmOncoX/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Nakken S.  (2024)  pharmOncoX: Targeted non-targeted anti-cancer drugs drug regimens.  R package version 1.6.4.  (https://github.com/sigven/pharmOncoX)","code":"@Manual{,   title = {pharmOncoX: Targeted and non-targeted anti-cancer drugs and drug regimens},   author = {Sigve Nakken},   year = {2024},   note = {R package version 1.6.4},   url = {https://github.com/sigven/pharmOncoX}, }"},{"path":"https://sigven.github.io/pharmOncoX/index.html","id":"pharmoncox-","dir":"","previous_headings":"","what":"Molecularly targeted cancer drugs and biomarkers","title":"Molecularly targeted cancer drugs and biomarkers","text":"pharmOncoX provides access targeted non-targeted cancer drugs, including comprehensive annotations per target, drug mechanism--action, approval dates, clinical trial phases various indications etc. data largely based drug-target-indication associations provided Open Targets Platform (Ochoa et al., Nucleic Acids Res., 2021). Associations retrieved Open Targets Platform integrated cancer-relevant indications/conditions (provided sigven/phenOncoX), allowing user retrieve drugs indicated main tumor types (e.g. Lung, Colon/Rectum etc.) Drug-target associations Open Targets Platform furthermore integrated appended drug information NCI Thesaurus, showing also non-targeted cancer drugs (chemotherapeutic agents etc.), various drug regimens. pharmOncoX provides anti-cancer drug classification existing entries Anatomical Therapeutic Chemical (ATC) Classification System, extended significantly manual curation, also establishing novel drug categories presently missing ATC classificiation tree (examples include AURK inhibitors, MET inhibitors, BET inhibitors, AKT inhibitors, PLK inhibitors, IAP inhibitors etc.) enabling filtering drugs according main mechanisms action. Currently (late February 2024), pharmOncoX built upon following releases external databases: Open Targets Platform (2023.12) ChEMBL (v33) NCI Thesaurus (24.01e)","code":""},{"path":"https://sigven.github.io/pharmOncoX/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Molecularly targeted cancer drugs and biomarkers","text":"Installation instructions Usage examples","code":""},{"path":"https://sigven.github.io/pharmOncoX/index.html","id":"contact","dir":"","previous_headings":"","what":"Contact","title":"Molecularly targeted cancer drugs and biomarkers","text":"sigven ifi.uio.","code":""},{"path":"https://sigven.github.io/pharmOncoX/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Molecularly targeted cancer drugs and biomarkers","text":"Please note project released Contributor Code Conduct. participating project agree abide terms.","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_biomarkers.html","id":null,"dir":"Reference","previous_headings":"","what":"Get curated cancer biomarker datasets — get_biomarkers","title":"Get curated cancer biomarker datasets — get_biomarkers","text":"Downloads preprocessed datasets local cache directory returns curated set genomic biomarkers multiple sources (CIViC, CGI, MitelmanDB) dataset comes list object, three elements: metadata - data frame metadata regarding drug resources used data - list four elements ('civic','cgi','mitelmandb','custom_fusions') fpath - path cache file","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_biomarkers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get curated cancer biomarker datasets — get_biomarkers","text":"","code":"get_biomarkers(cache_dir = NA, force_download = F)"},{"path":"https://sigven.github.io/pharmOncoX/reference/get_biomarkers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get curated cancer biomarker datasets — get_biomarkers","text":"cache_dir Local directory data download force_download Logical indicating local cache force downloaded (.e. set TRUE re-download even data exists cache)","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_biomarkers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get curated cancer biomarker datasets — get_biomarkers","text":"entry source-specific (e.g. 'civic') entry data list contains list three data frames: variant - list biomarker variants, extensively populated according variant aliases (identifer - column variant_id) clinical - cross-references variants recorded variant data frame clinical evidence items (identifier - column evidence_id) underlying literature evidence (identifier - column source_id) literature - lists literature source_id's listed clinical data frame","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drug_records.html","id":null,"dir":"Reference","previous_headings":"","what":"Function that retrieves pharmOncoX data from Google Drive — get_drug_records","title":"Function that retrieves pharmOncoX data from Google Drive — get_drug_records","text":"Function retrieves pharmOncoX data Google Drive","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drug_records.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that retrieves pharmOncoX data from Google Drive — get_drug_records","text":"","code":"get_drug_records(cache_dir = NA, force_download = F)"},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drug_records.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that retrieves pharmOncoX data from Google Drive — get_drug_records","text":"cache_dir Local directory data download force_download Logical indicating local cache force downloaded (.e. set TRUE re-download even data exists cache)","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drugs.html","id":null,"dir":"Reference","previous_headings":"","what":"Get antineoplastic drugs and drug regimens — get_drugs","title":"Get antineoplastic drugs and drug regimens — get_drugs","text":"Downloads preprocessed datasets local cache directory returns selected set drugs based various criteria set user. dataset comes list object, two elements: metadata - data frame metadata regarding drug resources used records - data frame drug records","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drugs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get antineoplastic drugs and drug regimens — get_drugs","text":"","code":"get_drugs(   cache_dir = NA,   force_download = FALSE,   exclude_salt_forms = TRUE,   exclude_adc = FALSE,   treatment_category = c(\"targeted_therapy_classified\", \"targeted_therapy_unclassified\",     \"chemo_therapy_classified\", \"hormone_therapy_classified\",     \"immuno_suppressants_classified\", \"other\"),   drug_is_approved = FALSE,   drug_target = NULL,   drug_action_type = NULL,   drug_indication_main = NULL,   drug_source_opentargets = FALSE,   drug_cancer_indication = TRUE,   drug_classified_cancer = TRUE,   drug_has_blackbox_warning = FALSE,   drug_approval_year = 1939,   drug_minimum_phase_any_indication = 0,   output_resolution = \"drug2target2indication\",   drug_action_inhibition = F )"},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drugs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get antineoplastic drugs and drug regimens — get_drugs","text":"cache_dir local cache directory data retrieval force_download force download data remote repository even data exists cache exclude_salt_forms exclude salt forms drugs exclude_adc exclude antibody-drug conjugates (ADCs) treatment_category main treatment category, classified according ATC ('targeted_therapy_classified', 'targeted_therapy_unclassified','chemo_therapy_classified','hormone_therapy_classified', 'immuno_suppressants_classified','') drug_is_approved logical indicating resulting drug records contain approved drugs drug_target character vector drug targets (gene symbols) drug records included results drug_action_type character vector drug action types include drug record list - possible values \"INHIBITOR\",\"AGONIST\",\"MODULATOR\",\"ANTAGONIST\", \"BLOCKER\",\"ACTIVATOR\",\"BINDING AGENT\",\"OPENER\", \"STABILISER\",\"CROSS-LINKING AGENT\",DISRUPTING AGENT\",\"\" drug_indication_main character vector main tumor types drug(s) indicated. Possible values: \"Adrenal Gland\",\"Biliary Tract\", \"Bladder/Urinary Tract\",\"Bone\",\"Breast\",\"Cervix\",\"CNS/Brain\", \"Colon/Rectum\",\"Esophagus/Stomach\",\"Eye\",\"Head Neck\",\"Kidney\", \"Liver\",\"Lung\",\"Lymphoid\",\"Myeloid\",\"Ovary/Fallopian Tube\", \"Pancreas\",\"Penis\",\"Peripheral Nervous System\",\"Peritoneum\", \"Pleura\",\"Prostate\",\"Skin\",\"Soft Tissue\",\"Testis\",\"Thymus\", \"Thyroid\",\"Uterus\",\"Vulva/Vagina\" drug_source_opentargets logical indicating resulting drug records contain drug records Open Targets Platform/ChEMBL drug_cancer_indication logical indicating resulting drug records indicated cancer conditions (approved conditions, found clinical trials etc.) drug_classified_cancer logical indicating resulting drug records classified \"L\" class ATC ( \"ANTINEOPLASTIC IMMUNOMODULATING AGENTS\") drug_has_blackbox_warning logical indicating resulting drug records contain drugs black box warnings drug_approval_year include records drugs approved later date (year) drug_minimum_phase_any_indication include drug records clinical phase (indication) greater equal phase output_resolution dictate output record resolution ('drug','drug2target','drug2target2indication') drug_action_inhibition logical indicating return drug records inhibitory mechanism--action","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_drugs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get antineoplastic drugs and drug regimens — get_drugs","text":"records data frame contains following columns (selected columns shown based value output_resolution) drug_id - drug identifier (pharmaOncoX) drug_name - primary drug name (upper case, NCI Thesaurus) drug_type - type drug molecule (Antibody, small molecule etc) molecule_chembl_id - ChEMBL compound identifier drug_action_type - main action elicited drug (antagonist, inhibitor, stabiliser etc) drug_alias - collection unambiguous drug aliases (separated '|') nci_concept_definition - detailed description drug mechanism--action (NCI Thesaurus) opentargets - logical - drug found Open Targets Platform resource is_salt - logical - drug record represents salt form (excluded default) is_adc - logical - drug record represents antibody-drug conjugate (ADC - excluded default) drug_blacbox_warning - logical indicating drug blackbox warning nci_t - NCI thesaurus identifier target_symbol - gene symbol drug target target_entrezgene - Entrez gene identifier drug target target_genename - gene name/description drug target target_ensembl_gene_id - Ensembl gene identifier drug target target_type - type drug target (single protein, protein family etc.) drug_max_phase_indication - maximum clinical phase drug (given indication) drug_approved_indication - logical indicating drug approved indication drug_frac_cancer_indications - fraction drug indications cancers drug_approved_noncancer - logical indicating drug approved non-cancer disease drug_n_indications - number indications given drug (approved indications, clinical trials etc) drug_year_first_approval - year drug first approved drug_max_ct_phase - maximum clinical phase drug (indication) disease_efo_id - EFO (Experimental Factor Ontology) identifier drug indication disease_efo_label - EFO (Experimental Factor Ontology) label drug indication primary_site - primary tumor site/type (obtained https://github.com/sigven/oncoPhenoMap) drug_clinical_id - drug clinical identifier (clinicaltrials.gov, DailyMed, FDA etc.) drug_clinical_source - underlying source drug entry (DailyMed, clinicaltrials.gov, FDA etc.) atc_code_level1 - drug identifier ATC (level 1) atc_level1 - drug label ATC (level 1) atc_code_level1 - drug identifier ATC (level 2) atc_level2 - drug label ATC (level 2) atc_code_level3 - drug identifier ATC (level 3) atc_level3 - drug label ATC (level 3) atc_treatment_category - treatment category (targeted/chemo/hormone, cancer/etc)","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_targeted_drugs.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to get on-label/off-label drugs (not complete) — get_targeted_drugs","title":"Utility function to get on-label/off-label drugs (not complete) — get_targeted_drugs","text":"Utility function get -label/-label drugs (complete)","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/get_targeted_drugs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to get on-label/off-label drugs (not complete) — get_targeted_drugs","text":"","code":"get_targeted_drugs(cache_dir = NA)"},{"path":"https://sigven.github.io/pharmOncoX/reference/get_targeted_drugs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to get on-label/off-label drugs (not complete) — get_targeted_drugs","text":"cache_dir Local cache directory","code":""},{"path":"https://sigven.github.io/pharmOncoX/reference/tidyeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy eval helpers — tidyeval","title":"Tidy eval helpers — tidyeval","text":"https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-164-april-30th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.6.4 (April 30th 2024)","title":"Version 1.6.4 (April 30th 2024)","text":"Improved clinical (tumor site) annotations fusions MitelmanDB","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-163-april-26th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.6.3 (April 26th 2024)","title":"Version 1.6.3 (April 26th 2024)","text":"Updated CIViC (20240426)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-162-april-12th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.6.2 (April 12th 2024)","title":"Version 1.6.2 (April 12th 2024)","text":"Updated NCI Thesaurus (24.03d)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-161-march-26th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.6.1 (March 26th 2024)","title":"Version 1.6.1 (March 26th 2024)","text":"Open Targets Platform update (v2024.03)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-160-march-9th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.6.0 (March 9th 2024)","title":"Version 1.6.0 (March 9th 2024)","text":"CIViC/Mitelmandb updates","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-159-february-29th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.5.9 (February 29th 2024)","title":"Version 1.5.9 (February 29th 2024)","text":"Updated CIViC","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-158-february-6th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.5.8 (February 6th 2024)","title":"Version 1.5.8 (February 6th 2024)","text":"NCI Thesaurus 24.01e","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-157-february-3rd-2024","dir":"Changelog","previous_headings":"","what":"Version 1.5.7 (February 3rd 2024)","title":"Version 1.5.7 (February 3rd 2024)","text":"Fixed buggy alias PubChem","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-156-january-31st-2024","dir":"Changelog","previous_headings":"","what":"Version 1.5.6 (January 31st 2024)","title":"Version 1.5.6 (January 31st 2024)","text":"Refine possible values treatment_category argument get_drugs() function Fix anti-androgen classification Fixed bug alias type notation copy numbers expression biomarkers Filter noise rank output helper function get_targeted_drugs Include variant primary name biomarker variants","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-150-january-25th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.5.0 (January 25th 2024)","title":"Version 1.5.0 (January 25th 2024)","text":"Considerable improvement drug classifications (output column atc_level3), considering targeted agents chemotherapy argument drug_targeted_agent renamed treatment_category helper function get_on_off_label_drugs renamed get_targeted_drugs","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-1410-january-17th-2024","dir":"Changelog","previous_headings":"","what":"Version 1.4.10 (January 17th 2024)","title":"Version 1.4.10 (January 17th 2024)","text":"Updated NCI Thesaurus (23.12d) Updated CIViC data (20240114) Revised manual drug classification (building upon ATC)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-148-december-12th-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.8 (December 12th 2023)","title":"Version 1.4.8 (December 12th 2023)","text":"Updated NCI Thesaurus - 23.11d Updated CIViC data (20231212)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-148-november-30th-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.8 (November 30th 2023)","title":"Version 1.4.8 (November 30th 2023)","text":"Updated OTP (v2023.12) Updated Mitelman database (20231016)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-147-november-3rd-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.7 (November 3rd 2023)","title":"Version 1.4.7 (November 3rd 2023)","text":"Fixed corrupt biomarker literature data frame","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-146-october-18th-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.6 (October 18th 2023)","title":"Version 1.4.6 (October 18th 2023)","text":"Fixed metadata Fixed -dated version descriptions (GH site) exclude compounds missing drug action type (platins etc.)","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-145-october-6th-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.5 (October 6th 2023)","title":"Version 1.4.5 (October 6th 2023)","text":"Updated NCI Thesaurus - 23.09d Updated CIViC data Added drug class (ATC) get_on_off_label_drugs()","code":""},{"path":"https://sigven.github.io/pharmOncoX/news/index.html","id":"version-144-september-1st-2023","dir":"Changelog","previous_headings":"","what":"Version 1.4.4 (September 1st 2023)","title":"Version 1.4.4 (September 1st 2023)","text":"Updated NCI Thesaurus - 23.08d Updated CIViC data Updated Mitelman database (20230803) get_biomarkers() now exported main function","code":""}]