Man pages for scuttle
Single-Cell RNA-Seq Analysis Utilities

addPerCellQCAdd QC metrics to a SummarizedExperiment
aggregateAcrossCellsAggregate data across groups of cells
aggregateAcrossFeaturesAggregate feature sets in a SummarizedExperiment
calculateAverageCalculate per-feature average counts
calculateCPMCalculate CPMs
calculateFPKMCalculate FPKMs
calculateTPMCalculate TPMs
downsampleBatchesDownsample batches to equal coverage
downsampleMatrixDownsample a count matrix
fitLinearModelFit a linear model
geometricSizeFactorsCompute geometric size factors
isOutlierIdentify outlier values
librarySizeFactorsCompute library size factors
logNormCountsCompute log-normalized expression values
makePerCellDFCreate a per-cell data.frame
makePerFeatureDFCreate a per-feature data.frame
medianSizeFactorsCompute median-based size factors
mockSCEMock up a SingleCellExperiment
normalizeCountsCompute normalized expression values
numDetectedAcrossCellsNumber of detected expression values per group of cells
numDetectedAcrossFeaturesNumber of detected expression values per group of features
perCellQCMetricsPer-cell quality control metrics
perFeatureQCMetricsPer-feature quality control metrics
quickPerCellQCQuick cell-level QC
readSparseCountsRead sparse count matrix from file
scuttle-pkgSingle-cell utilities
scuttle-utilsDeveloper utilities
sumCountsAcrossCellsSum expression across groups of cells
sumCountsAcrossFeaturesSum counts across feature sets
summarizeAssayByGroupSummarize an assay by group
uniquifyFeatureNamesMake feature names unique
whichNonZeroFind non-zero entries of a matrix
scuttle documentation built on Dec. 19, 2020, 2 a.m.