docs: update all experimental flags to stable flags

CogDisResLab · Sep 21, 2024 · a986e43 · a986e43
1 parent ce91f1f
commit a986e43
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Showing 19 changed files with 25 additions and 18 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -19,6 +19,7 @@
 ^doc$
 ^drugfindR\.Rproj$
 ^drugfindR\.code-workspace$
+^ltex\..*$
 ^raw$
 ^renovate\.json$
 ^renv$

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drugfindR
 Title: Investigate iLINCS for candidate repurposable drugs
-Version: 0.99.988
+Version: 0.99.989
 Authors@R: c(
     person(given = c("Ali", "Sajid"),
            family = "Imami",

diff --git a/R/consensusConcordants.R b/R/consensusConcordants.R
@@ -2,7 +2,7 @@
 NULL
 
 #' Generate a Consensus list of Targets
-#' `r lifecycle::badge("experimental")`
+#' `r lifecycle::badge("stable")`
 #'
 #' This function takes a list of (optionally split)
 #' concordance dataframes and returns

diff --git a/R/filterSignature.R b/R/filterSignature.R
@@ -1,5 +1,5 @@
 #' Filter the L1000 Signature
-#' `r lifecycle::badge("experimental")`
+#' `r lifecycle::badge("stable")`
 #'
 #' This function filters the L1000 Signature to a given threshold, identifying
 #' up-regulated or down-regulated or both up- and down-regulated genes

diff --git a/R/getConcordants.R b/R/getConcordants.R
@@ -1,5 +1,5 @@
 #' Get Concordant Signatures from iLINCS
-#' `r lifecycle::badge("experimental")`
+#' `r lifecycle::badge("stable")`
 #'
 #' This function takes a full or filtered signature
 #' and gets concordant signatures

diff --git a/R/getSignature.R b/R/getSignature.R
@@ -1,5 +1,5 @@
 #' Get the L1000 Signature from iLINCS
-#' `r lifecycle::badge("experimental")`
+#' `r lifecycle::badge("stable")`
 #'
 #' This function acts as the entrypoint to the iLINCS database.
 #' This takes in an ID and returns the signature after making a

diff --git a/R/investigateSignature.R b/R/investigateSignature.R
@@ -4,7 +4,7 @@
 NULL
 
 #' Investigate a given DGE dataset
-#' `r lifecycle::badge("experimental")`
+#' `r lifecycle::badge("stable")`
 #'
 #' This function takes a DGE Data frame and then
 #' finds concordant signatures to that.

diff --git a/R/investigateTarget.R b/R/investigateTarget.R
@@ -4,7 +4,7 @@
 NULL
 
 #' Investigate a Given Gene or Drug
-#' `r lifecycle::badge("experimental")`
+#' `r lifecycle::badge("stable")`
 #'
 #' This function takes the name of a gene or a drug and a
 #' database to use to pull signatures

diff --git a/R/prepareSignature.R b/R/prepareSignature.R
@@ -1,5 +1,5 @@
 #' Prepare an L1000 Signature froma given differential gene expression output
-#' `r lifecycle::badge("experimental")`
+#' `r lifecycle::badge("stable")`
 #'
 #' This function takes a differential gene expression output from any pipeline
 #' like edgeR or DeSeq2 or any that give you the gene symbol,

diff --git a/README.md b/README.md
@@ -5,8 +5,13 @@
 <!-- badges: start -->
 
 [![Lifecycle:
-experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+experimental](man/figures/lifecycle-stable.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 
+![GitHub repo size](https://img.shields.io/github/repo-size/CogDisResLab/drugfindR)
+![GitHub Issues or Pull Requests](https://img.shields.io/github/issues/CogDisResLab/drugfindR)
+![GitHub Issues or Pull Requests](https://img.shields.io/github/issues-pr/CogDisResLab/drugfindR)
+![Libraries.io dependency status for GitHub repo](https://img.shields.io/librariesio/github/CogDisResLab/drugfindR)
+[![CodeFactor](https://www.codefactor.io/repository/github/cogdisreslab/drugfindr/badge)](https://www.codefactor.io/repository/github/cogdisreslab/drugfindr)![REUSE Compliance](https://img.shields.io/reuse/compliance/github.com%2FCogDisResLab%2FdrugfindR.git)
 [![Continuous Integration / R
 Workflows](https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml/badge.svg)](https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml)
 [![latest-version](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fcogdisreslab.r-universe.dev%2Fapi%2Fpackages%2FdrugfindR&query=%24.Version&style=flat&label=latest-release&color=orange)](https://github.com/CogDisResLab/drugfindR/releases/latest)

diff --git 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": "0.99.988",
+  "version": "0.99.989",
   "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": "2087.012KB",
+  "fileSize": "2086.975KB",
   "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/WORDLIST b/inst/WORDLIST
@@ -1807,6 +1807,7 @@ COBLL
 COBLP
 COCH
 codecov
+CodeFactor
 codemeta
 codemetar
 codeRepository

diff --git a/man/consensusConcordants.Rd b/man/consensusConcordants.Rd
diff --git a/man/filterSignature.Rd b/man/filterSignature.Rd
diff --git a/man/getConcordants.Rd b/man/getConcordants.Rd
diff --git a/man/getSignature.Rd b/man/getSignature.Rd
diff --git a/man/investigateSignature.Rd b/man/investigateSignature.Rd
diff --git a/man/investigateTarget.Rd b/man/investigateTarget.Rd
diff --git a/man/prepareSignature.Rd b/man/prepareSignature.Rd