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scuttle

Single-Cell RNA-Seq Analysis Utilities


Bioconductor version: Release (3.18)

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 "4.3") 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")
1. Quality control HTML R Script
2. Normalization HTML R Script
3. Other functions HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends SingleCellExperiment
Imports methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat
System Requirements C++11
URL
See More
Suggests BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran
Linking To Rcpp, beachmat
Enhances
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, dreamlet, escheR, ggsc, HCAData, iSEEde, iSEEpathways, mastR, miloR, MouseThymusAgeing, raer, SCArray, schex, SingleR, TSCAN
Links To Me DropletUtils, scran
Build Report Build Report

Package Archives

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

Source Package scuttle_1.12.0.tar.gz
Windows Binary scuttle_1.12.0.zip (64-bit only)
macOS Binary (x86_64) scuttle_1.12.0.tgz
macOS Binary (arm64) scuttle_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scuttle
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scuttle
Bioc Package Browser https://code.bioconductor.org/browse/scuttle/
Package Short Url https://bioconductor.org/packages/scuttle/
Package Downloads Report Download Stats