Man pages for roryk/bcbioRnaseq
RNA-Seq Utilities

aggregateReplicatesAggregate Lane-Split Technical Replicates
AllGenericsS4 Generics
alphaSummaryPrint Summary Statistics of Alpha Level Cutoffs
annotableEnsembl Annotations
bcbiobcbioRNASeq Additional Run Data Accessor
bcbioRNADataSet-classbcbioRNADataSet Legacy Object Class
bcbioRNASeq-classbcbioRNASeq Object Class
bcbioRNASeq-packagebcbioRNASeq
coerceCoerce Object
colDataColumn Data
countsCount Matrix Accessors
deprecatedDeprecated Functions
designDesign Formula Accessor
flatFilesGet Flat Files from S4 Object
genderMarkersGender Marker Genes
gene2symbolGene to Symbol Mappings
interestingGroupsInteresting Groups
loadRNASeqLoad bcbio RNA-Seq Data
meltLog10Melt Count Matrix to Long Format and log10 Transform
metricsSample Metrics
plot53BiasPlot 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
plotHeatmapPlot Heatmap
plotIntronicMappingRatePlot Intronic Mapping Rate
plotMAPlot Mean Average
plotMappedReadsPlot Mapped Reads
plotMappingRatePlot Mapping Rate
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
resultsTablesDifferential Expression Results Tables
sampleMetadataSample Metadata
subsetBracket-Based Subsetting
tmmTrimmed Mean of M-Values (TMM) Normalization
topTablesTop Tables of Differential Expression Results
tpmTranscripts Per Million (TPM)
roryk/bcbioRnaseq documentation built on Dec. 13, 2017, 11:13 p.m.