first commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - '**'
+    paths-ignore:
+      - '*.md'
+      - '*.MD'
+      - '*.ignore'
+      - LICENSE
+
+jobs:
+
+  SigGenes:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - uses: actions/checkout@v4
+
+      # Run everything via the Bioconductor docker image as it has almost all dependencies preinstalled
+      - name: devtools-check-docker
+        run: |
+          bioc_install='BiocManager::install(c("edgeR", "limma", "Matrix", "S4Vectors", "scuttle", "SummarizedExperiment", "SingleCellExperiment"))'
+          dev_check='devtools::check("/SigGenes/")'
+          dev_doc='devtools::document("/SigGenes/")'
+          testthat='testthat::test_file("/SigGenes/tests/testthat/all_tests.R")'
+          docker run -v "$(pwd)":"/SigGenes/" bioconductor/bioconductor_docker:RELEASE_3_18 Rscript --vanilla -e "${bioc_install}; ${dev_check}; ${dev_doc}; ${testthat}"
+          docker run -v "$(pwd)":"/SigGenes/" bioconductor/bioconductor_docker:RELEASE_3_19 Rscript --vanilla -e "${bioc_install}; ${dev_check}; ${dev_doc}; ${testthat}"

.gitignore

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+..R*
+gitHeadInfo.gin
+R/.Rapp.history
+*.DS_*
+.Rproj.user
+.Rhistory
+~*
+*.tar.gz
+.Rproj.user

DESCRIPTION

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+Package: SigGenes
+Title: Automated differential analysis and signature generation for bulk and single-cell data
+Description: Automated differential analysis between groups based on limma-voom and generation of per-group signatures via custom filtering.
+Version: 1.0.0
+Author: Alexander Bender [aut,cre]
+Maintainer: Alexander Bender <[email protected]>
+License: LGPL (>=2)
+Encoding: UTF-8
+Depends:
+  R (>= 4.0),
+Imports: 
+  edgeR, 
+  limma,
+  Matrix,
+  methods,
+  S4Vectors, 
+  scuttle, 
+  SingleCellExperiment,
+  SummarizedExperiment
+Suggests:
+  testthat
+URL: https://github.com/atpoint/SigGenes
+BugReports: https://github.com/atpoint/SigGenes/issues
+RoxygenNote: 7.2.3

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(create_signatures)
+export(de_limma)
+export(get_pexpr)
+importFrom(Matrix,t)
+importFrom(S4Vectors,SimpleList)
+importFrom(SingleCellExperiment,"sizeFactors<-")
+importFrom(SingleCellExperiment,colData)
+importFrom(SingleCellExperiment,sizeFactors)
+importFrom(SummarizedExperiment,assay)
+importFrom(SummarizedExperiment,assayNames)
+importFrom(SummarizedExperiment,colData)
+importFrom(edgeR,DGEList)
+importFrom(edgeR,calcNormFactors)
+importFrom(edgeR,filterByExpr)
+importFrom(edgeR,voomLmFit)
+importFrom(limma,contrasts.fit)
+importFrom(limma,is.fullrank)
+importFrom(limma,makeContrasts)
+importFrom(limma,topTreat)
+importFrom(limma,treat)
+importFrom(methods,as)
+importFrom(methods,is)
+importFrom(scuttle,aggregateAcrossCells)
+importFrom(scuttle,librarySizeFactors)
+importFrom(stats,model.matrix)
+importFrom(utils,combn)

NEWS

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+CHANGES IN VERSION 1.0.0
+------------------------
+
+    o Initial commit