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✨
DESCRIPTION |NEWS
card.svg |card.png
scuttle/json (API)

# 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)

immunooncology singlecell rnaseq qualitycontrol preprocessing normalization transcriptomics geneexpression sequencing software dataimport openblas cpp

10.93 score 10 stars 98 packages 3.0k scripts 53 exports 30 dependencies

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

Target	Result	Time
bioc-checks	WARNING	527
linux-devel-arm64	WARNING	593
linux-devel-x86_64	WARNING	776
source / vignettes	OK	1159
linux-release-arm64	WARNING	628
linux-release-x86_64	WARNING	758
macos-release-arm64	WARNING	241
macos-release-x86_64	WARNING	653
macos-oldrel-arm64	WARNING	239
macos-oldrel-x86_64	WARNING	583
windows-devel	WARNING	1809
windows-release	WARNING	1872
windows-oldrel	WARNING	1907
wasm-release	OK	773

Exports:.assignIndicesToWorkers .bpNotSharedOrUp .guessMinMean .ranksafeQR .splitColsByWorkers .splitRowsByWorkers .splitVectorByWorkers .subset2index .unpackLists addPerCellQC addPerCellQCMetrics addPerFeatureQC addPerFeatureQCMetrics aggregateAcrossCells aggregateAcrossFeatures calculateAverage calculateCPM calculateFPKM calculateTPM cleanSizeFactors computeGeometricFactors computeLibraryFactors computeMedianFactors computePooledFactors computeSpikeFactors correctGroupSummary downsampleBatches downsampleMatrix fitLinearModel geometricSizeFactors isOutlier librarySizeFactors logNormCounts makePerCellDF makePerFeatureDF medianSizeFactors mockSCE normalizeCounts numDetectedAcrossCells numDetectedAcrossFeatures outlier.filter perCellQCFilters perCellQCMetrics perFeatureQCMetrics pooledSizeFactors quickPerCellQC readSparseCounts sumCountsAcrossCells sumCountsAcrossFeatures summarizeAssayByGroup uniquifyDataFrameByGroup uniquifyFeatureNames whichNonZero

Dependencies:abind assorthead beachmat BH Biobase BiocGenerics BiocParallel codetools cpp11 DelayedArray formatR futile.logger futile.options generics GenomicRanges IRanges lambda.r lattice Matrix MatrixGenerics matrixStats Rcpp S4Arrays S4Vectors Seqinfo SingleCellExperiment snow SparseArray SummarizedExperiment XVector

Legacy utilities for single-cell RNA-seq analysis

Rendered fromuserguide.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add QC metrics to a SummarizedExperiment	addPerCellQC addPerCellQCMetrics addPerFeatureQC addPerFeatureQCMetrics
Aggregate data across groups of cells	aggregateAcrossCells aggregateAcrossCells,SingleCellExperiment-method aggregateAcrossCells,SummarizedExperiment-method
Aggregate feature sets in a SummarizedExperiment	aggregateAcrossFeatures
Calculate per-feature average counts	calculateAverage calculateAverage,ANY-method calculateAverage,SingleCellExperiment-method calculateAverage,SummarizedExperiment-method
Calculate CPMs	calculateCPM calculateCPM,ANY-method calculateCPM,SingleCellExperiment-method calculateCPM,SummarizedExperiment-method
Calculate FPKMs	calculateFPKM
Calculate TPMs	calculateTPM calculateTPM,ANY-method calculateTPM,SingleCellExperiment-method calculateTPM,SummarizedExperiment-method
Clean out non-positive size factors	cleanSizeFactors
Normalization by deconvolution	computePooledFactors pooledSizeFactors pooledSizeFactors,ANY-method pooledSizeFactors,SummarizedExperiment-method
Normalization with spike-in counts	computeSpikeFactors
Correct group-level summaries	correctGroupSummary
Downsample batches to equal coverage	downsampleBatches
Downsample a count matrix	downsampleMatrix
Fit a linear model	fitLinearModel
Compute geometric size factors	computeGeometricFactors geometricSizeFactors geometricSizeFactors,ANY-method geometricSizeFactors,SummarizedExperiment-method
Identify outlier values	isOutlier outlier.filter outlier.filter-class [.outlier.filter
Compute library size factors	computeLibraryFactors librarySizeFactors librarySizeFactors,ANY-method librarySizeFactors,SummarizedExperiment-method
Compute log-normalized expression values	logNormCounts logNormCounts,SingleCellExperiment-method logNormCounts,SummarizedExperiment-method
Create a per-cell data.frame	makePerCellDF
Create a per-feature data.frame	makePerFeatureDF
Compute median-based size factors	computeMedianFactors medianSizeFactors medianSizeFactors,ANY-method medianSizeFactors,SummarizedExperiment-method
Mock up a SingleCellExperiment	mockSCE
Compute normalized expression values	normalizeCounts normalizeCounts,ANY-method normalizeCounts,SingleCellExperiment-method normalizeCounts,SummarizedExperiment-method
Number of detected expression values per group of cells	numDetectedAcrossCells numDetectedAcrossCells,ANY-method numDetectedAcrossCells,SummarizedExperiment-method
Number of detected expression values per group of features	numDetectedAcrossFeatures numDetectedAcrossFeatures,ANY-method numDetectedAcrossFeatures,SummarizedExperiment-method
Compute filters for low-quality cells	perCellQCFilters
Per-cell quality control metrics	perCellQCMetrics perCellQCMetrics,ANY-method perCellQCMetrics,SingleCellExperiment-method perCellQCMetrics,SummarizedExperiment-method
Per-feature quality control metrics	perFeatureQCMetrics perFeatureQCMetrics,ANY-method perFeatureQCMetrics,SummarizedExperiment-method
Quick cell-level QC	quickPerCellQC quickPerCellQC,ANY-method quickPerCellQC,SummarizedExperiment-method
Read sparse count matrix from file	readSparseCounts
Single-cell utilities	scuttle-pkg
Developer utilities	.assignIndicesToWorkers .bpNotSharedOrUp .checkCountMatrix .guessMinMean .ranksafeQR .splitColsByWorkers .splitRowsByWorkers .splitVectorByWorkers .subset2index .unpackLists scuttle-utils
Sum expression across groups of cells	sumCountsAcrossCells sumCountsAcrossCells,ANY-method sumCountsAcrossCells,SummarizedExperiment-method
Sum counts across feature sets	sumCountsAcrossFeatures sumCountsAcrossFeatures,ANY-method sumCountsAcrossFeatures,SummarizedExperiment-method
Summarize an assay by group	summarizeAssayByGroup summarizeAssayByGroup,ANY-method summarizeAssayByGroup,SummarizedExperiment-method
Groupwise unique rows of a DataFrame	uniquifyDataFrameByGroup
Make feature names unique	uniquifyFeatureNames