Man pages for acidgenomics/r-acidsinglecell
Acid Genomics Single Cell Experiment
| AcidSingleCell-package | AcidSingleCell |
| AcidSingleCellTestsUrl | AcidSingleCell test data URL |
| aggregate | Aggregate |
| aggregateCellsToSamples | Aggregate cells to samples |
| barcodeRanksPerSample | Barcode ranks per sample |
| cellCountsPerCluster | Cell counts per cluster |
| CellCycleMarkers | Cell-cycle markers |
| CellCycleMarkers-class | Cell-cycle markers |
| cellCycleMarkersList | Cell-cycle markers list |
| cellToSample | Cell-to-sample mappings |
| CellTypeMarkers | Cell-type markers |
| CellTypeMarkers-class | Cell-type markers |
| cellTypeMarkersList | Cell-type markers list |
| cellTypesPerCluster | Cell types per cluster |
| clusters | Cluster identifiers |
| combine | Combine multiple objects |
| convertSampleIdsToNames | Convert sample identifiers to names |
| cpm | Counts per million |
| diffExp | Differential expression |
| diffExpPerCluster | Differential expression per cluster |
| export | Export data from R |
| filterCells | Filter cells |
| findMarkers | Find cluster-specific marker genes |
| geometricMean | Geometric mean |
| indropsSampleIndexCounts | Get the inDrops sample index counts from i5 FASTQ files |
| KnownMarkers-class | Known markers |
| makeSingleCellExperiment | Make a SingleCellExperiment object |
| mapCellsToSamples | Map cells to samples |
| melt | Melt data from wide to long format |
| metrics | Quality control metrics |
| normalize | Normalize expression using pre-computed size factors |
| sampleData | Sample data |
| selectSamples | Select samples |
| show | Show an object |
| subsetPerSample | Subset per sample |
| topCellsPerSample | Top cells per sample |
| zerosVsDepth | Percentage of zeros vs. library depth |
