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
