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Bioconductor - scuttle

scuttle

This is the released version of scuttle; for the devel version, see scuttle.

Single-Cell RNA-Seq Analysis Utilities

Bioconductor version: Release (3.21)

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 1.18.0 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, singleCellTK, 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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