| .assignIndicesToWorkers | Developer utilities |
| .bpNotSharedOrUp | Developer utilities |
| .checkCountMatrix | Developer utilities |
| .guessMinMean | Developer utilities |
| .ranksafeQR | Developer utilities |
| .splitColsByWorkers | Developer utilities |
| .splitRowsByWorkers | Developer utilities |
| .splitVectorByWorkers | Developer utilities |
| .subset2index | Developer utilities |
| .unpackLists | Developer utilities |
| addPerCellQC | Add QC metrics to a SummarizedExperiment |
| addPerCellQCMetrics | Add QC metrics to a SummarizedExperiment |
| addPerFeatureQC | Add QC metrics to a SummarizedExperiment |
| addPerFeatureQCMetrics | Add QC metrics to a SummarizedExperiment |
| aggregateAcrossCells | Aggregate data across groups of cells |
| aggregateAcrossCells-method | Aggregate data across groups of cells |
| aggregateAcrossFeatures | Aggregate feature sets in a SummarizedExperiment |
| calculateAverage | Calculate per-feature average counts |
| calculateAverage-method | Calculate per-feature average counts |
| calculateCPM | Calculate CPMs |
| calculateCPM-method | Calculate CPMs |
| calculateFPKM | Calculate FPKMs |
| calculateTPM | Calculate TPMs |
| calculateTPM-method | Calculate TPMs |
| cleanSizeFactors | Clean out non-positive size factors |
| computeGeometricFactors | Compute geometric size factors |
| computeLibraryFactors | Compute library size factors |
| computeMedianFactors | Compute median-based size factors |
| computePooledFactors | Normalization by deconvolution |
| computeSpikeFactors | Normalization with spike-in counts |
| correctGroupSummary | Correct group-level summaries |
| downsampleBatches | Downsample batches to equal coverage |
| downsampleMatrix | Downsample a count matrix |
| fitLinearModel | Fit a linear model |
| geometricSizeFactors | Compute geometric size factors |
| geometricSizeFactors-method | Compute geometric size factors |
| isOutlier | Identify outlier values |
| librarySizeFactors | Compute library size factors |
| librarySizeFactors-method | Compute library size factors |
| logNormCounts | Compute log-normalized expression values |
| logNormCounts-method | 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 |
| medianSizeFactors-method | Compute median-based size factors |
| mockSCE | Mock up a SingleCellExperiment |
| normalizeCounts | Compute normalized expression values |
| normalizeCounts-method | Compute normalized expression values |
| numDetectedAcrossCells | Number of detected expression values per group of cells |
| numDetectedAcrossCells-method | Number of detected expression values per group of cells |
| numDetectedAcrossFeatures | Number of detected expression values per group of features |
| numDetectedAcrossFeatures-method | Number of detected expression values per group of features |
| outlier.filter | Identify outlier values |
| outlier.filter-class | Identify outlier values |
| perCellQCFilters | Compute filters for low-quality cells |
| perCellQCMetrics | Per-cell quality control metrics |
| perCellQCMetrics-method | Per-cell quality control metrics |
| perFeatureQCMetrics | Per-feature quality control metrics |
| perFeatureQCMetrics-method | Per-feature quality control metrics |
| pooledSizeFactors | Normalization by deconvolution |
| pooledSizeFactors-method | Normalization by deconvolution |
| quickPerCellQC | Quick cell-level QC |
| quickPerCellQC-method | 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 |
| sumCountsAcrossCells-method | Sum expression across groups of cells |
| sumCountsAcrossFeatures | Sum counts across feature sets |
| sumCountsAcrossFeatures-method | Sum counts across feature sets |
| summarizeAssayByGroup | Summarize an assay by group |
| summarizeAssayByGroup-method | Summarize an assay by group |
| uniquifyFeatureNames | Make feature names unique |
| [.outlier.filter | Identify outlier values |