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batchelor

This is the development version of batchelor; for the stable release version, see batchelor.

Single-Cell Batch Correction Methods

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.17.2
In Bioconductor since BioC 3.9 (R-3.6) (4.5 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
Linking To Rcpp
Suggests testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq
System Requirements C++11
Enhances
URL
See More
Depends On Me OSCA.advanced, OSCA.intro, OSCA.multisample, OSCA.workflows
Imports Me ChromSCape, mumosa, scMerge, 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_1.17.2.tar.gz
Windows Binary batchelor_1.17.2.zip
macOS Binary (x86_64) batchelor_1.17.2.tgz
macOS Binary (arm64)
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