Package: scuttle 1.23.1

Aaron Lun

scuttle: Legacy Utilities for Single-Cell RNA-Seq Analysis

Provides some legacy utility functions for performing single-cell analyses. Most of these functions are deprecated in favor of newer, more performant alternatives. We just keep this package around for back-compatibility and to point to the replacement functions.

Authors:Aaron Lun [aut, cre], Davis McCarthy [aut]

scuttle_1.23.1.tar.gz
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scuttle_1.23.1.tgz(r-4.6-x86_64)scuttle_1.23.1.tgz(r-4.6-arm64)scuttle_1.23.1.tgz(r-4.5-x86_64)scuttle_1.23.1.tgz(r-4.5-arm64)
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scuttle_1.23.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scuttle/json (API)
NEWS

# Install 'scuttle' in R:
install.packages('scuttle', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ltla/scuttle/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

On BioConductor:scuttle-1.23.1(bioc 3.24)scuttle-1.22.0(bioc 3.23)

immunooncologysinglecellrnaseqqualitycontrolpreprocessingnormalizationtranscriptomicsgeneexpressionsequencingsoftwaredataimportopenblascpp

12.16 score 10 stars 97 packages 3.0k scripts 17k downloads 53 exports 30 dependencies

Last updated from:88a483825e. Checks:12 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING278
linux-devel-arm64WARNING396
linux-devel-x86_64WARNING463
source / vignettesOK419
linux-release-arm64WARNING387
linux-release-x86_64WARNING465
macos-release-arm64WARNING412
macos-release-x86_64WARNING965
macos-oldrel-arm64WARNING276
macos-oldrel-x86_64WARNING523
windows-develWARNING2023
windows-releaseWARNING2028
windows-oldrelWARNING1898
wasm-releaseOK218

Exports:.assignIndicesToWorkers.bpNotSharedOrUp.guessMinMean.ranksafeQR.splitColsByWorkers.splitRowsByWorkers.splitVectorByWorkers.subset2index.unpackListsaddPerCellQCaddPerCellQCMetricsaddPerFeatureQCaddPerFeatureQCMetricsaggregateAcrossCellsaggregateAcrossFeaturescalculateAveragecalculateCPMcalculateFPKMcalculateTPMcleanSizeFactorscomputeGeometricFactorscomputeLibraryFactorscomputeMedianFactorscomputePooledFactorscomputeSpikeFactorscorrectGroupSummarydownsampleBatchesdownsampleMatrixfitLinearModelgeometricSizeFactorsisOutlierlibrarySizeFactorslogNormCountsmakePerCellDFmakePerFeatureDFmedianSizeFactorsmockSCEnormalizeCountsnumDetectedAcrossCellsnumDetectedAcrossFeaturesoutlier.filterperCellQCFiltersperCellQCMetricsperFeatureQCMetricspooledSizeFactorsquickPerCellQCreadSparseCountssumCountsAcrossCellssumCountsAcrossFeaturessummarizeAssayByGroupuniquifyDataFrameByGroupuniquifyFeatureNameswhichNonZero

Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocParallelcodetoolscpp11DelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicRangesIRangeslambda.rlatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSeqinfoSingleCellExperimentsnowSparseArraySummarizedExperimentXVector

Legacy utilities for single-cell RNA-seq analysis

Aaron Lun

Rendered fromuserguide.Rmdusingknitr::rmarkdownon Jun 10 2026.

Last update: 2026-04-06
Started: 2026-04-06

Readme and manuals

Help Manual

Help pageTopics
Add QC metrics to a SummarizedExperimentaddPerCellQC addPerCellQCMetrics addPerFeatureQC addPerFeatureQCMetrics
Aggregate data across groups of cellsaggregateAcrossCells aggregateAcrossCells,SingleCellExperiment-method aggregateAcrossCells,SummarizedExperiment-method
Aggregate feature sets in a SummarizedExperimentaggregateAcrossFeatures
Calculate per-feature average countscalculateAverage calculateAverage,ANY-method calculateAverage,SingleCellExperiment-method calculateAverage,SummarizedExperiment-method
Calculate CPMscalculateCPM calculateCPM,ANY-method calculateCPM,SingleCellExperiment-method calculateCPM,SummarizedExperiment-method
Calculate FPKMscalculateFPKM
Calculate TPMscalculateTPM calculateTPM,ANY-method calculateTPM,SingleCellExperiment-method calculateTPM,SummarizedExperiment-method
Clean out non-positive size factorscleanSizeFactors
Normalization by deconvolutioncomputePooledFactors pooledSizeFactors pooledSizeFactors,ANY-method pooledSizeFactors,SummarizedExperiment-method
Normalization with spike-in countscomputeSpikeFactors
Correct group-level summariescorrectGroupSummary
Downsample batches to equal coveragedownsampleBatches
Downsample a count matrixdownsampleMatrix
Fit a linear modelfitLinearModel
Compute geometric size factorscomputeGeometricFactors geometricSizeFactors geometricSizeFactors,ANY-method geometricSizeFactors,SummarizedExperiment-method
Identify outlier valuesisOutlier outlier.filter outlier.filter-class [.outlier.filter
Compute library size factorscomputeLibraryFactors librarySizeFactors librarySizeFactors,ANY-method librarySizeFactors,SummarizedExperiment-method
Compute log-normalized expression valueslogNormCounts logNormCounts,SingleCellExperiment-method logNormCounts,SummarizedExperiment-method
Create a per-cell data.framemakePerCellDF
Create a per-feature data.framemakePerFeatureDF
Compute median-based size factorscomputeMedianFactors medianSizeFactors medianSizeFactors,ANY-method medianSizeFactors,SummarizedExperiment-method
Mock up a SingleCellExperimentmockSCE
Compute normalized expression valuesnormalizeCounts normalizeCounts,ANY-method normalizeCounts,SingleCellExperiment-method normalizeCounts,SummarizedExperiment-method
Number of detected expression values per group of cellsnumDetectedAcrossCells numDetectedAcrossCells,ANY-method numDetectedAcrossCells,SummarizedExperiment-method
Number of detected expression values per group of featuresnumDetectedAcrossFeatures numDetectedAcrossFeatures,ANY-method numDetectedAcrossFeatures,SummarizedExperiment-method
Compute filters for low-quality cellsperCellQCFilters
Per-cell quality control metricsperCellQCMetrics perCellQCMetrics,ANY-method perCellQCMetrics,SingleCellExperiment-method perCellQCMetrics,SummarizedExperiment-method
Per-feature quality control metricsperFeatureQCMetrics perFeatureQCMetrics,ANY-method perFeatureQCMetrics,SummarizedExperiment-method
Quick cell-level QCquickPerCellQC quickPerCellQC,ANY-method quickPerCellQC,SummarizedExperiment-method
Read sparse count matrix from filereadSparseCounts
Single-cell utilitiesscuttle-pkg
Developer utilities.assignIndicesToWorkers .bpNotSharedOrUp .checkCountMatrix .guessMinMean .ranksafeQR .splitColsByWorkers .splitRowsByWorkers .splitVectorByWorkers .subset2index .unpackLists scuttle-utils
Sum expression across groups of cellssumCountsAcrossCells sumCountsAcrossCells,ANY-method sumCountsAcrossCells,SummarizedExperiment-method
Sum counts across feature setssumCountsAcrossFeatures sumCountsAcrossFeatures,ANY-method sumCountsAcrossFeatures,SummarizedExperiment-method
Summarize an assay by groupsummarizeAssayByGroup summarizeAssayByGroup,ANY-method summarizeAssayByGroup,SummarizedExperiment-method
Groupwise unique rows of a DataFrameuniquifyDataFrameByGroup
Make feature names uniqueuniquifyFeatureNames