scuttle
This is the released version of scuttle; for the devel version, see scuttle.
All Bioconductor versions of scuttle
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12
Legacy Utilities for Single-Cell RNA-Seq Analysis
Bioconductor version: 3.23 · Package version: 1.22.0
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.
Author: Aaron Lun [aut, cre], Davis McCarthy [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
Citation
From within R, enter citation("scuttle"):
Aaron Lun, Davis McCarthy. scuttle: Legacy Utilities for Single-Cell RNA-Seq Analysis. doi:10.18129/B9.bioc.scuttle, R package version 1.22.0, https://bioconductor.org/packages/scuttle.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scuttle")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.22.0 |
| License | GPL-3 |
| System Requirements | C++17 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 years) |
| Downloads rank | 64 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/scuttle/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scuttle")| Legacy utilities for single-cell RNA-seq analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | scuttle_1.22.0.tar.gz |
| Windows binary (x86_64) | scuttle_1.22.0.zip |
| macOS binary (arm64) | scuttle_1.22.0.tgz |
| macOS binary (x86_64) | scuttle_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scuttle |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scuttle |
| Package Downloads Report | Download Stats |
Dependencies
Depends: SingleCellExperiment
Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat
LinkingTo: Rcpp, beachmat, assorthead
Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran
Reverse dependencies
Depends On Me (3): omicsGMF, scater, scran
Imports Me (26): BASiCS, BASiCStan, batchelor, chevreulPlot, chevreulProcess, ClusterGVis, DESpace, DropletUtils, epiregulon, FLAMES, miaDash, mixhvg, mumosa, muscat, SanityR, scDblFinder, simPIC, singIST, singleCellTK, SpaceTrooper, SpatialArtifacts, spatialLIBD, splatter, SplineDV, spoon, velociraptor
Suggests Me (36): Banksy, bluster, CSOA, dreamlet, epiregulon.extra, escheR, futurize, ggsc, GSABenchmark, hammers, HCAData, iSEEde, iSEEfier, iSEEpathways, LISTO, mastR, mia, miloR, MouseThymusAgeing, raer, ReactomeGSA, SCArray, scConform, scCustomize, scDiagnostics, scDotPlot, schex, Seqtometry, SingleCellAlleleExperiment, sketchR, smoothclust, SpotSweeper, StatescopeR, SVP, tpSVG, TSCAN
Links To Me (2): DropletUtils, scran