Man pages for WeiSong-bio/roryk-bcbioSinglecell
Single-Cell RNA-Seq Utilities
| aggregateReplicates | Aggregate Replicates |
| all_markers_small | Sanitized Markers Example |
| barcodeRanksPerSample | Barcode Ranks per Sample |
| bcbio | Additional bcbio Run Data Accessor |
| bcbioSingleCell | 'bcbioSingleCell' Object and Constructor |
| bcbioSingleCell-package | bcbioSingleCell |
| cell2sample | Cell to Sample Mappings |
| cellCountsPerCluster | Cell Counts per Cluster |
| cellCycleMarkers | Cell-Cycle Markers |
| cellranger_small | Cell Ranger Example |
| cellTypeMarkers | Cell-Type Markers |
| cellTypesPerCluster | Cell Types per Cluster |
| clusterCellCountsPerSample | Cluster Cell Counts per Sample |
| coerce | Methods for Coercing an Object to a Class |
| defunct | Defunct Functions |
| deprecated | Deprecated Functions |
| diffExp | Differential Expression |
| extract | Extract or Replace Parts of an Object |
| fetchData | Fetch Data Functions |
| filterCells | Filter Cells |
| general | General Arguments |
| indrops_small | inDrops Example |
| knownMarkersDetected | Known Markers Detected |
| known_markers_small | Known Markers Example |
| mapCellsToSamples | Define Cell to Sample Mappings |
| metrics | Sample Barcode Metrics |
| metricsPerSample | Metrics per Sample |
| plotBarcodeRanks | Plot Barcode Ranks |
| plotCellCounts | Plot Cell Counts |
| plotCellTypesPerCluster | Plot Cell Types per Cluster |
| plotDimensionalReduction | Plot Dimensional Reduction |
| plotDot | Plot Dot |
| plotFeature | Plot Feature |
| plotGene | Plot Gene |
| plotGenesPerCell | Plot Genes per Cell |
| plotMarker | Plot Cell-Type-Specific Gene Markers |
| plotMitoRatio | Plot Mitochondrial Transcript Abundance |
| plotMitoVsCoding | Plot Mitochondrial vs. Coding Counts |
| plotNovelty | Plot Novelty Score |
| plotPCElbow | Plot PC Elbow |
| plotQC | Quality Control Plots |
| plotReadsPerCell | Plot Read Counts per Cell |
| plotUMIsPerCell | Plot UMIs per Cell |
| plotUMIsVsGenes | Plot UMI and Gene Correlation |
| plotViolin | Plot Violin |
| plotZerosVsDepth | Plot Percentage of Zeros vs. Library Depth |
| prepareSingleCellTemplate | Prepare Single-Cell RNA-Seq R Markdown Template |
| readCellRanger | Read 10X Genomics Cell Ranger Data |
| readCellTypeMarkers | Read Cell Type Markers File |
| reexports | Objects exported from other packages |
| sampleData | Sample Data |
| sanitizeMarkers | Sanitize Markers Output |
| selectSamples | Select Samples |
| seurat-SingleCellExperiment | Extend S4 Methods for 'seurat' Class |
| seurat_small | Seurat Example |
| show | Show an Object |
| subsetPerSample | Subset Per Sample |
| topBarcodes | Top Barcodes |
| topMarkers | Top Markers |
| updateObject | Update an Object to Its Current Class Definition |
