DOI: 10.18129/B9.bioc.scuttle  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see scuttle.

Single-Cell RNA-Seq Analysis Utilities

Bioconductor version: 3.17

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 "4.3") and enter:

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


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


biocViews DataImport, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.10.3
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL-3
Depends SingleCellExperiment
Imports methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat
LinkingTo Rcpp, beachmat
Suggests BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran
SystemRequirements C++11
Depends On Me scater, scran
Imports Me BASiCS, BASiCStan, batchelor, DropletUtils, FLAMES, imcRtools, mia, mumosa, muscat, scDblFinder, singleCellTK, spatialHeatmap, spatialLIBD, splatter, velociraptor
Suggests Me bluster, DESpace, HCAData, mastR, miloR, MouseThymusAgeing, SCArray, SingleR, TSCAN
Links To Me DropletUtils, scran
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Source Package scuttle_1.10.3.tar.gz
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macOS Binary (x86_64) scuttle_1.10.3.tgz
macOS Binary (arm64) scuttle_1.10.3.tgz
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