Man pages for steinbaugh/DESeqAnalysis
Acid Genomics DESeq2 Analysis Utilities

alphaSummaryAlpha level cutoff summary statistics
alphaThresholdAlpha threshold
apeglmResultsRun a quick pairwise contrast using lfcShrink with apeglm
baseBase methods
baseMeanThresholdBase mean threshold
coerceCoercion methods
combineCombine multiple objects
contrastNameContrast name
contrastSamplesSamples corresponding to a differential expression contrast
correlationCorrelation
degDifferentially expressed genes
degIntersectionIntersection of differentially expressed genes
degPerContrastBase mean threshold
deseqDESeq2 example analysis
DESeqAnalysisDESeq2 differential expression analysis
DESeqAnalysis-classDESeq2 differential expression analysis
DESeqAnalysisListList containing related DESeq2 analyses
DESeqAnalysisList-classList containing related DESeq2 analyses
DESeqAnalysis-packageDESeqAnalysis
deseqMinimalMinimal DESeq2 example analysis
DESeqResultsListList containing related DESeqResults objects
DESeqResultsList-classList containing related DESeqResults objects
exportExport
extractExtract or replace parts of an object
importPairwiseContrastsImport pairwise contrasts from a file
interestingGroupsInteresting groups
lfcShrinkShrink log2 fold changes
lfcShrinkTypeShrunken log2 fold change (LFC) type
lfcThresholdLog2 fold change threshold
markdownTablesMarkdown tables
matchMetadataToFilesMatch user metadata to file names used for tximport
paramsShared parameter documentation
plotBaseMeanPlot base mean distribution
plotContrastScatterPlot scatterplot of differential expression contrast
plotCountsPlot counts
plotDEGHeatmapDifferentially expressed gene heatmap
plotDEGPCAPlot differentially expressed gene principal component...
plotDEGStackedBarStacked bar plot of DEGs
plotDEGUpsetUpSet plot of directional DEG intersections across contrasts
plotHeatmapHeatmap
plotLFCPlot log2 fold change distributions
plotMAMA plot
plotPCAPrincipal component analysis plot
plotVolcanoVolcano plot
prepareTximportFilesPrepare quant files for tximport
resultsResults
resultsDiffRelative difference of results
resultsMatrixDESeq aggregate results matrix
resultsNamesResults names
resultsTablesResults tables
sampleDataSample data
showShow an object
transformTypeVariance-stabilizing transformation type
updateObjectUpdate object
steinbaugh/DESeqAnalysis documentation built on June 25, 2022, 7:29 a.m.