Acid Genomics Single Cell Experiment
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Documentation for package ‘AcidSingleCell’ version 0.3.5
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| aggregate | Aggregate |
| aggregate-method | Aggregate |
| aggregateCellsToSamples | Aggregate cells to samples |
| aggregateCellsToSamples-method | Aggregate cells to samples |
| barcodeRanksPerSample | Barcode ranks per sample |
| barcodeRanksPerSample-method | Barcode ranks per sample |
| cell2sample | Cell-to-sample mappings |
| cell2sample-method | Cell-to-sample mappings |
| cellCountsPerCluster | Cell counts per cluster |
| cellCountsPerCluster-method | Cell counts per cluster |
| CellCycleMarkers | Cell-cycle markers |
| CellCycleMarkers-class | Cell-cycle markers |
| cellCycleMarkersList | Cell-cycle markers list |
| CellTypeMarkers | Cell-type markers |
| CellTypeMarkers-class | Cell-type markers |
| cellTypeMarkersList | Cell-type markers list |
| cellTypesPerCluster | Cell types per cluster |
| cellTypesPerCluster-method | Cell types per cluster |
| clusters | Cluster identifiers |
| clusters-method | Cluster identifiers |
| combine | Combine multiple objects |
| combine-method | Combine multiple objects |
| convertSampleIDsToNames | Convert sample identifiers to names |
| convertSampleIDsToNames-method | Convert sample identifiers to names |
| diffExp | Differential expression |
| diffExp-method | Differential expression |
| diffExpPerCluster | Differential expression per cluster |
| diffExpPerCluster-method | Differential expression per cluster |
| export | Export |
| export-method | Export |
| filterCells | Filter cells |
| filterCells-method | Filter cells |
| findMarkers | Find cluster-specific marker genes |
| findMarkers-method | Find cluster-specific marker genes |
| geometricMean | Geometric mean |
| geometricMean-method | Geometric mean |
| importCellCycleMarkers | Cell-cycle markers |
| importCellTypeMarkers | Cell-type markers |
| KnownMarkers-class | Known markers |
| makeSingleCellExperiment | Make a SingleCellExperiment object |
| mapCellsToSamples | Map cells to samples |
| melt | Melt data from wide to long format |
| melt-method | Melt data from wide to long format |
| metrics | Quality control metrics |
| metrics-method | Quality control metrics |
| metricsPerSample | Quality control metrics |
| metricsPerSample-method | Quality control metrics |
| normalize | Normalize expression using pre-computed size factors |
| normalize-method | Normalize expression using pre-computed size factors |
| sampleData | Sample data |
| sampleData-method | Sample data |
| sampleData<- | Sample data |
| sampleData<--method | Sample data |
| selectSamples | Select samples |
| selectSamples-method | Select samples |
| show | Show an object |
| show-method | Show an object |
| subsetPerSample | Subset per sample |
| subsetPerSample-method | Subset per sample |
| topCellsPerSample | Top cells per sample |
| topCellsPerSample-method | Top cells per sample |
| zerosVsDepth | Percentage of zeros vs. library depth |
| zerosVsDepth-method | Percentage of zeros vs. library depth |