From a986e43c7651db89958c8541cc334fe57166a1ec Mon Sep 17 00:00:00 2001 From: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com> Date: Sat, 21 Sep 2024 17:12:55 -0400 Subject: [PATCH] docs: update all experimental flags to stable flags --- .Rbuildignore | 1 + DESCRIPTION | 2 +- R/consensusConcordants.R | 2 +- R/filterSignature.R | 2 +- R/getConcordants.R | 2 +- R/getSignature.R | 2 +- R/investigateSignature.R | 2 +- R/investigateTarget.R | 2 +- R/prepareSignature.R | 2 +- README.md | 7 ++++++- codemeta.json | 4 ++-- inst/WORDLIST | 1 + man/consensusConcordants.Rd | 2 +- man/filterSignature.Rd | 2 +- man/getConcordants.Rd | 2 +- man/getSignature.Rd | 2 +- man/investigateSignature.Rd | 2 +- man/investigateTarget.Rd | 2 +- man/prepareSignature.Rd | 2 +- 19 files changed, 25 insertions(+), 18 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index f1ddb27..8022ca3 100644 --- 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 index b2e8fe8..4cc6a78 100644 --- 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 index 5f621f2..2c02a2c 100644 --- 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 index 2b0db98..0458ede 100644 --- 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 index 1372265..f1021f1 100644 --- 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 index 84e289a..459fd48 100644 --- 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 index 5b5cc24..62c4456 100644 --- 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 index 8b4ca48..8699264 100644 --- 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 index 59529a8..ae73fd6 100644 --- 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 index 33f5144..88a4c7b 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,13 @@ [![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 index dc96b2a..6563eec 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": "0.99.988", + "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 index 399a70b..f8b6c12 100644 --- 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 index fda3225..56facc4 100644 --- a/man/consensusConcordants.Rd +++ b/man/consensusConcordants.Rd @@ -3,7 +3,7 @@ \name{consensusConcordants} \alias{consensusConcordants} \title{Generate a Consensus list of Targets -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}} +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}} \usage{ consensusConcordants(..., paired = FALSE, cutoff = 0.321, cellLine = NULL) } diff --git a/man/filterSignature.Rd b/man/filterSignature.Rd index 6307c37..a52aa5a 100644 --- a/man/filterSignature.Rd +++ b/man/filterSignature.Rd @@ -3,7 +3,7 @@ \name{filterSignature} \alias{filterSignature} \title{Filter the L1000 Signature -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}} +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}} \usage{ filterSignature(signature, direction = "any", threshold = NULL, prop = NULL) } diff --git a/man/getConcordants.Rd b/man/getConcordants.Rd index 7e35830..c5b6268 100644 --- a/man/getConcordants.Rd +++ b/man/getConcordants.Rd @@ -3,7 +3,7 @@ \name{getConcordants} \alias{getConcordants} \title{Get Concordant Signatures from iLINCS -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}} +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}} \usage{ getConcordants(signature, ilincsLibrary = "CP") } diff --git a/man/getSignature.Rd b/man/getSignature.Rd index 86af159..503f9fc 100644 --- a/man/getSignature.Rd +++ b/man/getSignature.Rd @@ -3,7 +3,7 @@ \name{getSignature} \alias{getSignature} \title{Get the L1000 Signature from iLINCS -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}} +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}} \usage{ getSignature(sigId, l1000 = TRUE) } diff --git a/man/investigateSignature.Rd b/man/investigateSignature.Rd index fc107b1..70baabe 100644 --- a/man/investigateSignature.Rd +++ b/man/investigateSignature.Rd @@ -3,7 +3,7 @@ \name{investigateSignature} \alias{investigateSignature} \title{Investigate a given DGE dataset -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}} +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}} \usage{ investigateSignature( expr, diff --git a/man/investigateTarget.Rd b/man/investigateTarget.Rd index 70ed0c2..6fa6193 100644 --- a/man/investigateTarget.Rd +++ b/man/investigateTarget.Rd @@ -3,7 +3,7 @@ \name{investigateTarget} \alias{investigateTarget} \title{Investigate a Given Gene or Drug -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}} +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}} \usage{ investigateTarget( target, diff --git a/man/prepareSignature.Rd b/man/prepareSignature.Rd index 8598cf0..c8af43e 100644 --- a/man/prepareSignature.Rd +++ b/man/prepareSignature.Rd @@ -3,7 +3,7 @@ \name{prepareSignature} \alias{prepareSignature} \title{Prepare an L1000 Signature froma given differential gene expression output -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}} +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}} \usage{ prepareSignature( dge,