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| bcbioRNASeq-package | bcbioRNASeq |
| aggregateReplicates | Aggregate Replicates |
| aggregateReplicates-method | Aggregate Replicates |
| alphaSummary | Alpha Level Cutoff Summary Statistics |
| alphaSummary-method | Alpha Level Cutoff Summary Statistics |
| as | Methods for Coercing an Object to a Class |
| bcbioRNASeq | 'bcbioRNASeq' Object and Constructor |
| bcbioRNASeq-class | 'bcbioRNASeq' Object and Constructor |
| bcb_small | 'bcbioRNASeq' Example |
| coerce | Methods for Coercing an Object to a Class |
| coerce-method | Methods for Coercing an Object to a Class |
| contrastName | Contrast Name |
| contrastName-method | Contrast Name |
| counts | Count Matrix Accessors |
| counts-method | Count Matrix Accessors |
| dds_small | 'DESeqDataSet' Example |
| extract | Extract or Replace Parts of an Object |
| loadRNASeq | 'bcbioRNASeq' Object and Constructor |
| metrics | Sample Metrics |
| metrics-method | Sample Metrics |
| plot5Prime3PrimeBias | Plot 5'->3' Bias |
| plot5Prime3PrimeBias-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 |
| plotDEGPCA | Plot DEG PCA |
| plotDEGPCA-method | Plot DEG PCA |
| 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 |
| plotIntronicMappingRate | Plot Intronic Mapping Rate |
| plotIntronicMappingRate-method | Plot Intronic Mapping Rate |
| plotMA | MA Plot |
| plotMA-method | MA Plot |
| plotMappedReads | Plot Mapped Reads |
| plotMappedReads-method | Plot Mapped Reads |
| plotMappingRate | Plot Mapping Rate |
| plotMappingRate-method | Plot Mapping Rate |
| plotMeanAverage | MA Plot |
| 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 |
| resultsTables | Differential Expression Results Tables |
| resultsTables-method | Differential Expression Results Tables |
| res_small | 'DESeqResults' Example |
| sampleData | Sample Data |
| sampleData-method | Sample Data |
| sampleData<- | Sample Data |
| sampleData<--method | Sample Data |
| show | Show an Object |
| show-method | Show an Object |
| tmm | *T*rimmed *M*ean of *M*-Values (TMM) Normalization |
| tmm-method | *T*rimmed *M*ean of *M*-Values (TMM) Normalization |
| 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) |
| updateObject | Update an Object to Its Current Class Definition |
| updateObject-method | Update an Object to Its Current Class Definition |
| [-method | Extract or Replace Parts of an Object |