batchelor

DOI: 10.18129/B9.bioc.batchelor  

Single-Cell Batch Correction Methods

Bioconductor version: Release (3.16)

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 "4.2") 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 1.14.1
In Bioconductor since BioC 3.9 (R-3.6) (4 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_1.14.1.tar.gz
Windows Binary batchelor_1.14.1.zip (64-bit only)
macOS Binary (x86_64) batchelor_1.14.1.tgz
macOS Binary (arm64) batchelor_1.14.1.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
Old Source Packages for BioC 3.16 Source Archive

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