Man pages for hbc/bcbioRnaseq
RNA-Seq Utilities

aggregateReplicatesAggregate Replicates
alphaSummaryAlpha Level Cutoff Summary Statistics
bcbioRNASeq'bcbioRNASeq' Object and Constructor
bcb_small'bcbioRNASeq' Example
coerceMethods for Coercing an Object to a Class
contrastNameContrast Name
countsCount Matrix Accessors
dds_small'DESeqDataSet' Example
deprecatedDefunct or Deprecated Functions
extractExtract or Replace Parts of an Object
genderMarkersGender Marker Genes
generalGeneral Arguments
metricsSample Metrics
plot5Prime3PrimeBiasPlot 5'->3' Bias
plotCorrelationHeatmapPlot Correlation Heatmap
plotCountDensityPlot Count Density
plotCountsPerGenePlot Counts Per Gene
plotDEGHeatmapDifferentially Expressed Gene Heatmap
plotDispEstsPlot Dispersion Estimates
plotExonicMappingRatePlot Exonic Mapping Rate
plotGenderMarkersPlot Sexually Dimorphic Gender Markers
plotGenePlot Individual Genes
plotGeneSaturationPlot Gene Detection Saturation
plotGenesDetectedPlot Genes Detected
plotIntronicMappingRatePlot Intronic Mapping Rate
plotMappedReadsPlot Mapped Reads
plotMappingRatePlot Mapping Rate
plotMeanAveragePlot Mean Average
plotMeanSDPlot Row Standard Deviations vs. Row Means
plotPCASample PCA Plot for Transformed Data
plotPCACovariatesFind Correlation Between Principal Components (PCs) and...
plotRRNAMappingRatePlot Ribosomal RNA (rRNA) Mapping Rate
plotTotalReadsPlot Total Reads
plotVolcanoPlot Volcano
prepareRNASeqTemplatePrepare RNA-Seq R Markdown Template
reexportsObjects exported from other packages
res_small'DESeqResults' Example
resultsTablesDifferential Expression Results Tables
rld_small'DESeqTransform' Example
showShow an Object
tmm*T*rimmed *M*ean of *M*-Values (TMM) Normalization
topTablesTop Tables of Differential Expression Results
tpmTranscripts Per Million (TPM)
updateObjectUpdate an Object to Its Current Class Definition
hbc/bcbioRnaseq documentation built on June 26, 2018, 7:17 a.m.