batchelor

Single-Cell Batch Correction Methods

Bioconductor version: Release (3.20)

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>

Citation (from within R, enter citation("batchelor")):

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.22.0
In Bioconductor since	BioC 3.9 (R-3.6) (5.5 years)
License	GPL-3
Depends	SingleCellExperiment
Imports	SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, SparseArray, DelayedArray(>= 0.31.5), DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat
System Requirements	C++11
URL

Suggests	testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq
Linking To	Rcpp
Enhances
Depends On Me	OSCA.intro, OSCA.workflows
Imports Me	ChromSCape, mumosa, scMerge, singleCellTK, SCIntRuler
Suggests Me	TSCAN, Canek, RaceID
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	batchelor_1.22.0.tar.gz
Windows Binary (x86_64)	batchelor_1.22.0.zip
macOS Binary (x86_64)	batchelor_1.22.0.tgz
macOS Binary (arm64)	batchelor_1.21.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/batchelor
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/batchelor
Bioc Package Browser	https://code.bioconductor.org/browse/batchelor/
Package Short Url	https://bioconductor.org/packages/batchelor/
Package Downloads Report	Download Stats