Man pages for scuttle
Single-Cell RNA-Seq Analysis Utilities
| addPerCellQC | Add QC metrics to a SummarizedExperiment |
| aggregateAcrossCells | Aggregate data across groups of cells |
| aggregateAcrossFeatures | Aggregate feature sets in a SummarizedExperiment |
| calculateAverage | Calculate per-feature average counts |
| calculateCPM | Calculate CPMs |
| calculateFPKM | Calculate FPKMs |
| calculateTPM | Calculate TPMs |
| downsampleBatches | Downsample batches to equal coverage |
| downsampleMatrix | Downsample a count matrix |
| fitLinearModel | Fit a linear model |
| geometricSizeFactors | Compute geometric size factors |
| isOutlier | Identify outlier values |
| librarySizeFactors | Compute library size factors |
| logNormCounts | Compute log-normalized expression values |
| makePerCellDF | Create a per-cell data.frame |
| makePerFeatureDF | Create a per-feature data.frame |
| medianSizeFactors | Compute median-based size factors |
| mockSCE | Mock up a SingleCellExperiment |
| normalizeCounts | Compute normalized expression values |
| numDetectedAcrossCells | Number of detected expression values per group of cells |
| numDetectedAcrossFeatures | Number of detected expression values per group of features |
| perCellQCMetrics | Per-cell quality control metrics |
| perFeatureQCMetrics | Per-feature quality control metrics |
| quickPerCellQC | Quick cell-level QC |
| readSparseCounts | Read sparse count matrix from file |
| scuttle-pkg | Single-cell utilities |
| scuttle-utils | Developer utilities |
| sumCountsAcrossCells | Sum expression across groups of cells |
| sumCountsAcrossFeatures | Sum counts across feature sets |
| summarizeAssayByGroup | Summarize an assay by group |
| uniquifyFeatureNames | Make feature names unique |
| whichNonZero | Find non-zero entries of a matrix |
