From 61e2a67e1006296296b1f8c38d1527f533b3c968 Mon Sep 17 00:00:00 2001 From: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com> Date: Sat, 21 Sep 2024 13:07:04 -0400 Subject: [PATCH 1/2] docs: add a documentation file for the `dCovid_diffexp.tsv` file Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com> --- DESCRIPTION | 2 +- codemeta.json | 4 ++-- inst/script/dCovid_diffexp.R | 19 +++++++++++++++++++ 3 files changed, 22 insertions(+), 3 deletions(-) create mode 100644 inst/script/dCovid_diffexp.R diff --git a/DESCRIPTION b/DESCRIPTION index 09adced..e2ad358 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: drugfindR Title: Investigate iLINCS for candidate repurposable drugs -Version: 0.99.986 +Version: 0.99.987 Authors@R: c( person(given = c("Ali", "Sajid"), family = "Imami", diff --git a/codemeta.json b/codemeta.json index 8c53b02..3ef088c 100644 --- a/codemeta.json +++ b/codemeta.json @@ -7,7 +7,7 @@ "codeRepository": "https://github.com/CogDisResLab/drugfindR", "issueTracker": "https://github.com/CogDisResLab/drugfindR/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "0.99.986", + "version": "0.99.987", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -350,7 +350,7 @@ "applicationCategory": "Genomics", "isPartOf": "https://bioconductor.org", "keywords": ["LINCS", "iLINCS", "drugrepurposing", "drugdiscovery", "transcriptomics", "geneexpression", "geneknockdown", "geneoverexpression", "chemicalperturbagen", "drugfindR", "r", "ilincs", "bioinformatics", "bioinformatics-pipeline"], - "fileSize": "2085.479KB", + "fileSize": "2086.498KB", "releaseNotes": "https://github.com/CogDisResLab/drugfindR/blob/master/NEWS.md", "readme": "https://github.com/CogDisResLab/drugfindR/blob/devel/README.md", "contIntegration": ["https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml", "https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel"], diff --git a/inst/script/dCovid_diffexp.R b/inst/script/dCovid_diffexp.R new file mode 100644 index 0000000..56bc501 --- /dev/null +++ b/inst/script/dCovid_diffexp.R @@ -0,0 +1,19 @@ +# This script servers as both documentation and script to downlaod +# the data file dCovid_diffexp.tsv from Zenodo. +# +# This file is used in the vignette to demonstrate the use of the +# drugfindR package. + +# The file that we download is part of a set of differential gene expression +# files that are located in the Zenodo repository at the following URL: +# https://zenodo.org/record/10265182 +# These files were generated by the author, who is also the author of the +# publication "Identification of candidate repurposable drugs to combat COVID‑19 using a signature‑based approach" (https://doi.org/10.1038/s41598-021-84044-9). +# +# This particular file contains the differential gene expression data for the +# patients with COVID-19 compared to the healthy controls. +url <- "https://zenodo.org/records/10265182/files/dCovid_diffexp.tsv" + +# We download the file to the inst/extdata directory of the package. +location <- file.path("inst", "extdata", "dCovid_diffexp.tsv") +download.file(url, location, method = "auto") From 0a382ed30fd5c05473140c72c12e05fe0636ccf3 Mon Sep 17 00:00:00 2001 From: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com> Date: Sat, 21 Sep 2024 13:19:13 -0400 Subject: [PATCH 2/2] docs(README): fix spelling errors in the README.md --- DESCRIPTION | 2 +- README.md | 8 ++++---- codemeta.json | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e2ad358..b2e8fe8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: drugfindR Title: Investigate iLINCS for candidate repurposable drugs -Version: 0.99.987 +Version: 0.99.988 Authors@R: c( person(given = c("Ali", "Sajid"), family = "Imami", diff --git a/README.md b/README.md index ae1514e..33f5144 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,6 @@ - -# drugfindR +# drugfindR: An R package to search iLINCS databases for small molecules @@ -15,6 +14,7 @@ Workflows](https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflow [![DOI](https://zenodo.org/badge/338354715.svg)](https://zenodo.org/badge/latestdoi/338354715) [![Codecov test coverage](https://codecov.io/gh/CogDisResLab/drugfindR/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel) + drugfindR allows convenient access to the iLINCS Gene Knockdown, Gene @@ -27,7 +27,7 @@ drugs. You can install the released version of drugfindR from [r-universe](https://cogdisreslab.r-universe.dev/drugfindR) with: -``` r +```r install.packages("drugfindR", repos = c( "https://cogdisreslab.r-universe.dev", @@ -38,7 +38,7 @@ install.packages("drugfindR", And the development version from [GitHub](https://github.com/) with: -``` r +```r if (!requireNamespace("devtools", quietly = TRUE)) { install.packages("devtools") } diff --git a/codemeta.json b/codemeta.json index 3ef088c..dc96b2a 100644 --- a/codemeta.json +++ b/codemeta.json @@ -7,7 +7,7 @@ "codeRepository": "https://github.com/CogDisResLab/drugfindR", "issueTracker": "https://github.com/CogDisResLab/drugfindR/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "0.99.987", + "version": "0.99.988", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -350,7 +350,7 @@ "applicationCategory": "Genomics", "isPartOf": "https://bioconductor.org", "keywords": ["LINCS", "iLINCS", "drugrepurposing", "drugdiscovery", "transcriptomics", "geneexpression", "geneknockdown", "geneoverexpression", "chemicalperturbagen", "drugfindR", "r", "ilincs", "bioinformatics", "bioinformatics-pipeline"], - "fileSize": "2086.498KB", + "fileSize": "2087.012KB", "releaseNotes": "https://github.com/CogDisResLab/drugfindR/blob/master/NEWS.md", "readme": "https://github.com/CogDisResLab/drugfindR/blob/devel/README.md", "contIntegration": ["https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml", "https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel"],