scuttle

DOI: 10.18129/B9.bioc.scuttle  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scuttle.

Single-Cell RNA-Seq Analysis Utilities

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DataImport, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.8.4
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL-3
Depends	SingleCellExperiment
Imports	methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat
LinkingTo	Rcpp, beachmat
Suggests	BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran
SystemRequirements	C++11
Enhances
URL
Depends On Me	scater, scran
Imports Me	BASiCS, BASiCStan, batchelor, DropletUtils, FLAMES, imcRtools, mia, mumosa, muscat, scDblFinder, singleCellTK, spatialHeatmap, spatialLIBD, velociraptor
Suggests Me	bluster, HCAData, miloR, MouseThymusAgeing, SingleR, splatter, TSCAN
Links To Me	DropletUtils, scran
Build Report

Package Archives

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

Source Package	scuttle_1.8.4.tar.gz
Windows Binary	scuttle_1.8.4.zip
macOS Binary (x86_64)	scuttle_1.8.4.tgz
macOS Binary (arm64)	scuttle_1.8.4.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