Single-Cell RNA-Seq Analysis Utilities

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Documentation for package ‘scuttle’ version 1.8.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.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