This is the development version of scuttle; for the stable release version, see scuttle.
Single-Cell RNA-Seq Analysis UtilitiesBioconductor version: Development (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, entercitation("scuttle")
): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scuttle")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo 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 1.19.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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 URL See More Suggests BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran Linking To Rcpp, beachmat Enhances Depends On Me 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, mumosa, muscat, scDblFinder, simPIC, splatter, SplineDV, spoon, velociraptor, spatialLIBD, mixhvg, SpatialDDLS Suggests Me Banksy, bluster, dreamlet, epiregulon.extra, escheR, ggsc, iSEEde, iSEEfier, iSEEpathways, mastR, miloR, raer, ReactomeGSA, SCArray, scDiagnostics, scDotPlot, schex, SingleCellAlleleExperiment, SingleR, sketchR, smoothclust, spatialHeatmap, SpotSweeper, SVP, tpSVG, TSCAN, HCAData, MouseThymusAgeing, scCustomize Links To Me DropletUtils, scran Build Report Build Report Package Archives
Follow Installation instructions to use this package in your R session.
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