Man pages for WeiSong-bio/roryk-bcbioRNASeq
RNA-Seq Utilities
| alphaSummary | Alpha Level Cutoff Summary Statistics |
| bcbioRNASeq-class | 'bcbioRNASeq' Object and Constructor |
| bcbioRNASeq-package | bcbioRNASeq |
| bcb_small | 'bcbioRNASeq' Example |
| coerce | Methods for Coercing an Object to a Class |
| contrastName | Contrast Name |
| counts | Count Matrix Accessors |
| dds_small | 'DESeqDataSet' Example |
| deprecated | Defunct or Deprecated Functions |
| genderMarkers | Gender Marker Genes |
| general | General Arguments |
| metrics | Sample Metrics |
| plot5Prime3PrimeBias | Plot 5'->3' Bias |
| plotCorrelationHeatmap | Plot Correlation Heatmap |
| plotCountDensity | Plot Count Density |
| plotCountsPerGene | Plot Counts Per Gene |
| plotDEGHeatmap | Differentially Expressed Gene Heatmap |
| plotDEGPCA | Plot DEG PCA |
| plotDispEsts | Plot Dispersion Estimates |
| plotExonicMappingRate | Plot Exonic Mapping Rate |
| plotGenderMarkers | Plot Sexually Dimorphic Gender Markers |
| plotGene | Plot Individual Genes |
| plotGeneSaturation | Plot Gene Detection Saturation |
| plotGenesDetected | Plot Genes Detected |
| plotIntronicMappingRate | Plot Intronic Mapping Rate |
| plotMappedReads | Plot Mapped Reads |
| plotMappingRate | Plot Mapping Rate |
| plotMeanAverage | Plot Mean Average |
| plotMeanSD | Plot Row Standard Deviations vs. Row Means |
| plotPCA | Sample PCA Plot for Transformed Data |
| plotPCACovariates | Find Correlation Between Principal Components (PCs) and... |
| plotRRNAMappingRate | Plot Ribosomal RNA (rRNA) Mapping Rate |
| plotTotalReads | Plot Total Reads |
| plotVolcano | Plot Volcano |
| prepareRNASeqTemplate | Prepare RNA-Seq R Markdown Template |
| reexports | Objects exported from other packages |
| res_small | 'DESeqResults' Example |
| resultsTables | Differential Expression Results Tables |
| rld_small | 'DESeqTransform' Example |
| show | Show an Object |
| subset | Bracket-Based Subsetting |
| tmm | Trimmed Mean of M-Values (TMM) Normalization |
| topTables | Top Tables of Differential Expression Results |
| tpm | Transcripts Per Million (TPM) |
| updateObject | Update Object |
