Files in steinbaugh/DESeqAnalysis

Acid Genomics DESeq2 Analysis Utilities

.Rbuildignore

.gitignore

.lintr

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/AllClasses.R R/AllGenerics.R R/AllGlobals.R R/DESeqAnalysis.R R/DESeqAnalysisList-methods.R R/DESeqResultsList-methods.R R/alphaSummary-methods.R R/alphaThreshold-methods.R R/apeglmResults-methods.R R/base-methods.R R/baseMeanThreshold-methods.R R/coerce-methods.R R/combine-methods.R R/contrastName-methods.R R/contrastSamples-methods.R R/correlation-methods.R R/data.R R/deg-methods.R R/degIntersection-methods.R R/degPerContrast-methods.R R/export-methods.R R/extract-methods.R R/importPairwiseContrasts.R R/interestingGroups-methods.R R/internal.R R/lfcShrink-methods.R R/lfcShrinkType-methods.R R/lfcThreshold-methods.R R/markdownTables-methods.R R/package.R R/params.R R/plotBaseMean-methods.R R/plotContrastScatter-methods.R R/plotCounts-methods.R R/plotDegHeatmap-methods.R R/plotDegPca-methods.R R/plotDegStackedBar-methods.R R/plotDegUpset-methods.R R/plotHeatmap-methods.R R/plotLfc-methods.R R/plotMa-methods.R R/plotPca-methods.R R/plotVolcano-methods.R R/prepareTximportFiles.R R/results-methods.R R/resultsDiff-methods.R R/resultsMatrix-methods.R R/resultsNames-methods.R R/resultsTables-methods.R R/sampleData-methods.R R/sanitizeTximportIdentifiers.R R/show-methods.R R/transformType-methods.R R/updateObject-methods.R README.md

_pkgdown.yml

data-raw/deseq.R data-raw/deseqMinimal.R

data/deseq.rda

data/deseqMinimal.rda

inst/extdata/contrasts.csv

inst/rmarkdown/templates/differential-expression/skeleton/.gitignore

inst/rmarkdown/templates/differential-expression/skeleton/skeleton.Rmd

inst/rmarkdown/templates/differential-expression/template.yaml

inst/scripts/render.R man/DESeqAnalysis-class.Rd man/DESeqAnalysis-package.Rd man/DESeqAnalysis.Rd man/DESeqAnalysisList-class.Rd man/DESeqAnalysisList.Rd man/DESeqResultsList-class.Rd man/DESeqResultsList.Rd man/alphaSummary.Rd man/alphaThreshold.Rd man/apeglmResults.Rd man/base.Rd man/baseMeanThreshold.Rd man/coerce.Rd man/combine.Rd man/contrastName.Rd man/contrastSamples.Rd man/correlation.Rd man/deg.Rd man/degIntersection.Rd man/degPerContrast.Rd man/deseq.Rd man/deseqMinimal.Rd man/export.Rd man/extract.Rd man/importPairwiseContrasts.Rd man/interestingGroups.Rd man/lfcShrink.Rd man/lfcShrinkType.Rd man/lfcThreshold.Rd man/markdownTables.Rd man/params.Rd man/plotBaseMean.Rd man/plotContrastScatter.Rd man/plotCounts.Rd man/plotDegHeatmap.Rd man/plotDegPca.Rd man/plotDegStackedBar.Rd man/plotDegUpset.Rd man/plotHeatmap.Rd man/plotLfc.Rd man/plotMa.Rd man/plotPca.Rd man/plotVolcano.Rd man/prepareTximportFiles.Rd man/results.Rd man/resultsDiff.Rd man/resultsMatrix.Rd man/resultsNames.Rd man/resultsTables.Rd man/sampleData.Rd man/sanitizeTximportIdentifiers.Rd man/show.Rd man/transformType.Rd man/updateObject.Rd

package.Rproj

pkgdown/extra.css

tests/testthat.R tests/testthat/helper-globals.R tests/testthat/test-DESeqAnalysis.R tests/testthat/test-DESeqAnalysisList.R tests/testthat/test-alphaSummary.R tests/testthat/test-alphaThreshold.R tests/testthat/test-baseMeanThreshold.R tests/testthat/test-combine.R tests/testthat/test-contrastName.R tests/testthat/test-contrastSamples.R tests/testthat/test-degIntersection.R tests/testthat/test-export.R tests/testthat/test-importPairwiseContrasts.R tests/testthat/test-lfcThreshold.R tests/testthat/test-markdownTables.R tests/testthat/test-plotContrastScatter.R tests/testthat/test-plotCounts.R tests/testthat/test-plotDegHeatmap.R tests/testthat/test-plotDegPca.R tests/testthat/test-plotDegStackedBar.R tests/testthat/test-plotDegUpset.R tests/testthat/test-plotLfc.R tests/testthat/test-plotMa.R tests/testthat/test-plotPca.R tests/testthat/test-plotVolcano.R tests/testthat/test-prepareTximportFiles.R tests/testthat/test-results.R tests/testthat/test-resultsMatrix.R tests/testthat/test-resultsNames.R tests/testthat/test-resultsTables.R tests/testthat/test-rmarkdown.R tests/testthat/test-sampleData.R tests/testthat/test-sanitizeTximportIdentifiers.R tests/testthat/test-show.R tests/testthat/test-transformType.R tests/testthat/test-updateObject.R

todo.org

steinbaugh/DESeqAnalysis documentation built on April 1, 2024, 8:30 a.m.