scuttle

DOI: 10.18129/B9.bioc.scuttle    

This is the development version of scuttle; to use it, please install the devel version of Bioconductor.

Single-Cell RNA-Seq Analysis Utilities

Bioconductor version: Development (3.12)

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 "4.0") and enter:

if (!requireNamespace("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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scuttle")

 

HTML R Script Package overview
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 0.99.14
In Bioconductor since BioC 3.12 (R-4.0)
License GPL-3
Depends SingleCellExperiment
Imports methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat
LinkingTo Rcpp, beachmat
Suggests BiocStyle, knitr, scRNAseq, rmarkdown, testthat
SystemRequirements C++11
Enhances
URL
Depends On Me
Imports Me batchelor, DropletUtils, scater, scDblFinder, scran
Suggests Me bluster, HCAData, SingleR, snifter, TSCAN
Links To Me DropletUtils, scran
Build Report  

Package Archives

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

Source Package scuttle_0.99.14.tar.gz
Windows Binary scuttle_0.99.14.zip
macOS 10.13 (High Sierra) scuttle_0.99.13.tgz
Source Repository git clone https://git.bioconductor.org/packages/scuttle
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scuttle
Package Short Url https://bioconductor.org/packages/scuttle/
Package Downloads Report Download Stats

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