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This is the development version of scuttle; for the stable release version, see scuttle.

Single-Cell RNA-Seq Analysis Utilities

Bioconductor version: Development (3.20)

Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.

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

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at>

Citation (from within R, enter citation("scuttle")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1. Quality control HTML R Script
2. Normalization HTML R Script
3. Other functions HTML R Script
Reference Manual PDF


biocViews DataImport, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.15.2
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends SingleCellExperiment
Imports methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat
System Requirements C++11
See More
Suggests BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran
Linking To Rcpp, beachmat
Depends On Me scater, scran, OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows
Imports Me BASiCS, BASiCStan, batchelor, DropletUtils, epiregulon, FLAMES, imcRtools, mia, mumosa, muscat, scDblFinder, simPIC, singleCellTK, spatialHeatmap, splatter, spoon, velociraptor, spatialLIBD, digitalDLSorteR, mixhvg, SpatialDDLS
Suggests Me Banksy, bluster, DESpace, dreamlet, epiregulon.extra, escheR, ggsc, iSEEde, iSEEfier, iSEEpathways, mastR, miloR, raer, SCArray, scDotPlot, schex, SingleCellAlleleExperiment, SingleR, sketchR, smoothclust, SpotSweeper, tpSVG, TSCAN, HCAData, MouseThymusAgeing, scCustomize
Links To Me DropletUtils, scran
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Follow Installation instructions to use this package in your R session.

Source Package scuttle_1.15.2.tar.gz
Windows Binary
macOS Binary (x86_64) scuttle_1.15.0.tgz
macOS Binary (arm64) scuttle_1.15.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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