Registration Open for Bioc2024 July 24-26


Single-Cell Batch Correction Methods

Bioconductor version: Release (3.19)

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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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

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


biocViews BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.20.0
In Bioconductor since BioC 3.9 (R-3.6) (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
System Requirements C++11
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq
Linking To Rcpp
Depends On Me OSCA.advanced, OSCA.intro, OSCA.multisample, 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_1.20.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) batchelor_1.20.0.tgz
macOS Binary (arm64) batchelor_1.20.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats