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| bcbioRNASeq-package | bcbioRNASeq |
| alphaSummary | Print Summary Statistics of Alpha Level Cutoffs |
| alphaSummary-method | Print Summary Statistics of Alpha Level Cutoffs |
| annotable | Ensembl Annotations |
| annotable-method | Ensembl Annotations |
| bcbio | bcbioRNASeq Additional Run Data Accessor |
| bcbio-method | bcbioRNASeq Additional Run Data Accessor |
| bcbio<--method | bcbioRNASeq Additional Run Data Accessor |
| bcbioRNASeq | bcbioRNASeq Object Class |
| bcbioRNASeq-class | bcbioRNASeq Object Class |
| coerce | Coerce Object |
| coerce-bcbioRNASeq-SummarizedExperiment | Coerce Object |
| colData | Column Data |
| colData<--method | Column Data |
| counts | Count Matrix Accessors |
| counts-method | Count Matrix Accessors |
| design | Design Formula Accessor |
| design-method | Design Formula Accessor |
| design<--method | Design Formula Accessor |
| flatFiles | Get Flat Files from S4 Object |
| flatFiles-method | Get Flat Files from S4 Object |
| gene2symbol | Gene to Symbol Mappings |
| gene2symbol-method | Gene to Symbol Mappings |
| interestingGroups | Interesting Groups |
| interestingGroups-method | Interesting Groups |
| interestingGroups<--method | Interesting Groups |
| loadRNASeq | Load bcbio RNA-Seq Data |
| meltLog10 | Melt Count Matrix to Long Format and log10 Transform |
| meltLog10-method | Melt Count Matrix to Long Format and log10 Transform |
| metrics | Sample Metrics |
| metrics-method | Sample Metrics |
| plot53Bias | Plot 5'->3' Bias |
| plot53Bias-method | Plot 5'->3' Bias |
| plotCorrelationHeatmap | Plot Correlation Heatmap |
| plotCorrelationHeatmap-method | Plot Correlation Heatmap |
| plotCountDensity | Plot Count Density |
| plotCountDensity-method | Plot Count Density |
| plotCountsPerGene | Plot Counts Per Gene |
| plotCountsPerGene-method | Plot Counts Per Gene |
| plotDEGHeatmap | Differentially Expressed Gene Heatmap |
| plotDEGHeatmap-method | Differentially Expressed Gene Heatmap |
| plotDispEsts | Plot Dispersion Estimates |
| plotDispEsts-method | Plot Dispersion Estimates |
| plotExonicMappingRate | Plot Exonic Mapping Rate |
| plotExonicMappingRate-method | Plot Exonic Mapping Rate |
| plotGenderMarkers | Plot Sexually Dimorphic Gender Markers |
| plotGenderMarkers-method | Plot Sexually Dimorphic Gender Markers |
| plotGene | Plot Individual Genes |
| plotGene-method | Plot Individual Genes |
| plotGeneSaturation | Plot Gene Detection Saturation |
| plotGeneSaturation-method | Plot Gene Detection Saturation |
| plotGenesDetected | Plot Genes Detected |
| plotGenesDetected-method | Plot Genes Detected |
| plotHeatmap | Plot Heatmap |
| plotHeatmap-method | Plot Heatmap |
| plotIntronicMappingRate | Plot Intronic Mapping Rate |
| plotIntronicMappingRate-method | Plot Intronic Mapping Rate |
| plotMA | Plot Mean Average |
| plotMA-method | Plot Mean Average |
| plotMappedReads | Plot Mapped Reads |
| plotMappedReads-method | Plot Mapped Reads |
| plotMappingRate | Plot Mapping Rate |
| plotMappingRate-method | Plot Mapping Rate |
| plotMeanSD | Plot Row Standard Deviations vs. Row Means |
| plotMeanSD-method | Plot Row Standard Deviations vs. Row Means |
| plotPCA | Sample PCA Plot for Transformed Data |
| plotPCA-method | Sample PCA Plot for Transformed Data |
| plotPCACovariates | Find Correlation Between Principal Components (PCs) and Covariates |
| plotPCACovariates-method | Find Correlation Between Principal Components (PCs) and Covariates |
| plotRRNAMappingRate | Plot Ribosomal RNA (rRNA) Mapping Rate |
| plotRRNAMappingRate-method | Plot Ribosomal RNA (rRNA) Mapping Rate |
| plotTotalReads | Plot Total Reads |
| plotTotalReads-method | Plot Total Reads |
| plotVolcano | Plot Volcano |
| plotVolcano-method | Plot Volcano |
| prepareRNASeqTemplate | Prepare RNA-Seq R Markdown Template |
| prepareRNASeqTemplate-method | Prepare RNA-Seq R Markdown Template |
| resultsTables | Differential Expression Results Tables |
| resultsTables-method | Differential Expression Results Tables |
| sampleMetadata | Sample Metadata |
| sampleMetadata-method | Sample Metadata |
| selectSamples | Select Samples |
| selectSamples-method | Select Samples |
| subset | Bracket-Based Subsetting |
| topTables | Top Tables of Differential Expression Results |
| topTables-method | Top Tables of Differential Expression Results |
| tpm | Transcripts Per Million (TPM) |
| tpm-method | Transcripts Per Million (TPM) |
| upgrade-bcbioRNASeq | Coerce Object |
| [-method | Bracket-Based Subsetting |