This is the released version of scuttle; for the devel version, see
scuttle.
Single-Cell RNA-Seq Analysis Utilities
Bioconductor version: Release (3.22)
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 gmail.com>
Citation (from within R, enter citation("scuttle")):
Installation
To install this package, start R (version "4.5") 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.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scuttle")
Details
biocViews
DataImport,
GeneExpression,
ImmunoOncology,
Normalization,
Preprocessing,
QualityControl,
RNASeq,
Sequencing,
SingleCell,
Software,
Transcriptomics
Version
1.20.0
In Bioconductor since
BioC 3.12 (R-4.0) (5 years)
License
GPL-3
Imports
methods, utils, stats,
Matrix,
Rcpp,
BiocGenerics,
S4Vectors,
BiocParallel,
GenomicRanges,
SummarizedExperiment,
S4Arrays,
MatrixGenerics,
SparseArray,
DelayedArray,
beachmat
System Requirements
C++11
See More
Enhances
Depends On Me
omicsGMF,
scater,
scran, OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, SingleRBook
Imports Me
BASiCS,
BASiCStan,
batchelor,
chevreulPlot,
chevreulProcess,
DESpace,
DropletUtils,
epiregulon,
FLAMES,
imcRtools,
mia,
miaDash,
mumosa,
muscat,
SanityR,
scDblFinder,
simPIC,
singleCellTK,
SpaceTrooper,
splatter,
SplineDV,
spoon,
velociraptor,
spatialLIBD, OSTA,
mixhvg,
SpatialDDLS
Suggests Me
Banksy,
bluster,
CSOA,
dreamlet,
epiregulon.extra,
escheR,
ggsc,
GSVA,
iSEEde,
iSEEfier,
iSEEpathways,
mastR,
miloR,
raer,
ReactomeGSA,
SCArray,
scDiagnostics,
scDotPlot,
schex,
SingleCellAlleleExperiment,
SingleR,
sketchR,
smoothclust,
SpotSweeper,
SVP,
tpSVG,
TSCAN,
HCAData,
MouseThymusAgeing,
scCustomize
Package Archives
Follow Installation instructions to use this package in your R session.
Source Repository
git clone https://git.bioconductor.org/packages/scuttle
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/scuttle