scuttle

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

All versions

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: Development (3.24)

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 1.23.2, 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")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("scuttle")

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

Documentation

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

browseVignettes("scuttle")

Single-cell utilities	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.23.2
In Bioconductor since	BioC 3.12 (R-4.0) (6 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++17
URL	https://github.com/LTLA/scuttle
Bug Reports	https://github.com/LTLA/scuttle/issues

Suggests	BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran
Linking To	Rcpp, beachmat, assorthead
Enhances
Depends On Me	omicsGMF, OSCA.advanced, OSCA.intro, OSCA.workflows, scater, scran, SingleRBook
Imports Me	BASiCS, BASiCStan, batchelor, BiocDuckDB, chevreulPlot, chevreulProcess, ClusterGVis, DESpace, DropletUtils, FLAMES, miaDash, mixhvg, mumosa, muscat, OSTA, SanityR, simPIC, singIST, SpaceTrooper, SpatialArtifacts, spatialLIBD, splatter, SplineDV, spoon, velociraptor
Suggests Me	Banksy, BenchHub, CSOA, dreamlet, epiregulon, epiregulon.extra, escheR, futurize, ggsc, GSABenchmark, hammers, HCAData, iSEEde, iSEEfier, iSEEpathways, LISTO, mastR, mia, miloR, MouseThymusAgeing, OMA, SCArray, scCompoundDE, scConform, scCustomize, scDiagnostics, scDotPlot, scFastDE, schex, Seqtometry, SingleCellAlleleExperiment, sketchR, smoothclust, SpotSweeper, StatescopeR, SVP, tpSVG, TSCAN
Links To Me	DropletUtils, scran
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scuttle_1.23.2.tar.gz
Windows Binary (x86_64)	scuttle_1.23.2.zip (64-bit only)
macOS Binary (big-sur-x86_64)	scuttle_1.23.2.tgz
macOS Binary (sonoma-arm64)	scuttle_1.23.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scuttle
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scuttle
Package Short Url	https://bioconductor.org/packages/scuttle/
Package Downloads Report	Download Stats