# Acid Genomics DESeq2 Analysis Utilities

## Documentation for package ‘DESeqAnalysis’ version 0.7.1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E I L M P R S T U misc

## -- A --

alphaSummary | Alpha level cutoff summary statistics
alphaSummary-method | Alpha level cutoff summary statistics
alphaThreshold | Alpha threshold
alphaThreshold-method | Alpha threshold
alphaThreshold<- | Alpha threshold
alphaThreshold<--method | Alpha threshold
apeglmResults | Run a quick pairwise contrast using lfcShrink with apeglm
apeglmResults-method | Run a quick pairwise contrast using lfcShrink with apeglm
as.DESeqDataSet | Coercion methods
as.DESeqDataSet-method | Coercion methods
as.DESeqTransform | Coercion methods
as.DESeqTransform-method | Coercion methods

## -- B --

baseMeanThreshold | Base mean threshold
baseMeanThreshold-method | Base mean threshold
baseMeanThreshold<- | Base mean threshold
baseMeanThreshold<--method | Base mean threshold

## -- C --

coerce | Coercion methods
coerce-method | Coercion methods
combine | Combine multiple objects
combine-method | Combine multiple objects
contrastName | Contrast name
contrastName-method | Contrast name
contrastName<- | Contrast name
contrastName<--method | Contrast name
contrastSamples | Samples corresponding to a differential expression contrast
contrastSamples-method | Samples corresponding to a differential expression contrast
correlation | Correlation
correlation-method | Correlation

## -- D --

deg | Differentially expressed genes
deg-method | Differentially expressed genes
degIntersection | Intersection of differentially expressed genes
degIntersection-method | Intersection of differentially expressed genes
degPerContrast | Base mean threshold
degPerContrast-method | Base mean threshold
deseq | DESeq2 example analysis
DESeqAnalysis | DESeq2 differential expression analysis
DESeqAnalysis-class | DESeq2 differential expression analysis
DESeqAnalysisList | List containing related DESeq2 analyses
DESeqAnalysisList-class | List containing related DESeq2 analyses
DESeqAnalysisList-method | List containing related DESeq2 analyses
deseqMinimal | Minimal DESeq2 example analysis
DESeqResultsList | List containing related DESeqResults objects
DESeqResultsList-class | List containing related DESeqResults objects
DESeqResultsList-method | List containing related DESeqResults objects

## -- E --

export | Export data from R
export-method | Export data from R
extract | Extract or replace parts of an object

## -- I --

importPairwiseContrasts | Import pairwise contrasts from a file
interestingGroups | Interesting groups
interestingGroups-method | Interesting groups
interestingGroups<- | Interesting groups
interestingGroups<--method | Interesting groups

## -- L --

lfcShrink | Shrink log2 fold changes
lfcShrink-method | Shrink log2 fold changes
lfcShrink<- | Shrink log2 fold changes
lfcShrink<--method | Shrink log2 fold changes
lfcShrinkType | Shrunken log2 fold change (LFC) type
lfcShrinkType-method | Shrunken log2 fold change (LFC) type
lfcThreshold | Log2 fold change threshold
lfcThreshold-method | Log2 fold change threshold
lfcThreshold<- | Log2 fold change threshold
lfcThreshold<--method | Log2 fold change threshold

## -- M --

markdownTables | Markdown tables
markdownTables-method | Markdown tables

## -- P --

plotBaseMean | Plot base mean distribution
plotBaseMean-method | Plot base mean distribution
plotContrastScatter | Plot scatterplot of differential expression contrast
plotContrastScatter-method | Plot scatterplot of differential expression contrast
plotCorrelationHeatmap | Heatmap
plotCorrelationHeatmap-method | Heatmap
plotCounts | Plot counts
plotCounts-method | Plot counts
plotDegHeatmap | Differentially expressed gene heatmap
plotDegHeatmap-method | Differentially expressed gene heatmap
plotDegPca | Plot differentially expressed gene principal component analysis
plotDegPca-method | Plot differentially expressed gene principal component analysis
plotDegStackedBar | Stacked bar plot of DEGs
plotDegStackedBar-method | Stacked bar plot of DEGs
plotDegUpset | UpSet plot of directional DEG intersections across contrasts
plotDegUpset-method | UpSet plot of directional DEG intersections across contrasts
plotHeatmap | Heatmap
plotHeatmap-method | Heatmap
plotLfc | Plot log2 fold change distributions
plotLfc-method | Plot log2 fold change distributions
plotMa | MA plot
plotMa-method | MA plot
plotPca | Principal component analysis plot
plotPca-method | Principal component analysis plot
plotQuantileHeatmap | Heatmap
plotQuantileHeatmap-method | Heatmap
plotVolcano | Volcano plot
plotVolcano-method | Volcano plot
prepareTximportFiles | Prepare quant files for tximport

## -- R --

results | Results
results-method | Results
resultsDiff | Relative difference of results
resultsDiff-method | Relative difference of results
resultsMatrix | DESeq aggregate results matrix
resultsMatrix-method | DESeq aggregate results matrix
resultsNames | Results names
resultsNames-method | Results names
resultsNames<- | Results names
resultsNames<--method | Results names
resultsTables | Results tables
resultsTables-method | Results tables

## -- S --

sampleData | Sample data
sampleData-method | Sample data
sanitizeTximportIdentifiers | Sanitize tximport identifiers
show | Show an object
show-method | Show an object

## -- T --

transformType | Variance-stabilizing transformation type
transformType-method | Variance-stabilizing transformation type

## -- U --

updateObject | Update object
updateObject-method | Update object

## -- misc --

[-method | Extract or replace parts of an object