addPerCellQCMetrics     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
cleanSizeFactors        Clean out non-positive 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
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
perCellQCFilters        Compute filters for low-quality cells
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
