batchelor

DOI: 10.18129/B9.bioc.batchelor    

Single-Cell Batch Correction Methods

Bioconductor version: Release (3.15)

Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression values. Functions are also provided to perform global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across batches.

Author: Aaron Lun [aut, cre], Laleh Haghverdi [ctb]

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("batchelor")

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("batchelor")

 

HTML	R Script	1. Correcting batch effects
HTML	R Script	2. Extending methods
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.12.3
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 years)
License	GPL-3
Depends	SingleCellExperiment
Imports	SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, DelayedArray, DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat
LinkingTo	Rcpp
Suggests	testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq
SystemRequirements	C++11
Enhances
URL
Depends On Me	OSCA.advanced, OSCA.intro, OSCA.multisample, OSCA.workflows
Imports Me	ChromSCape, mumosa, singleCellTK
Suggests Me	TSCAN
Links To Me
Build Report

Package Archives

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

Source Package	batchelor_1.12.3.tar.gz
Windows Binary	batchelor_1.12.3.zip (64-bit only)
macOS Binary (x86_64)	batchelor_1.12.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/batchelor
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/batchelor
Package Short Url	https://bioconductor.org/packages/batchelor/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive