batchelor

DOI: 10.18129/B9.bioc.batchelor    

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

Single-Cell Batch Correction Methods

Bioconductor version: Development (3.12)

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 "4.0") and enter:

if (!requireNamespace("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")

 

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 1.5.5
In Bioconductor since BioC 3.9 (R-3.6) (1.5 years)
License GPL-3
Depends SingleCellExperiment
Imports SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, DelayedArray, DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix
LinkingTo Rcpp, beachmat
Suggests testthat, BiocStyle, knitr, beachmat, scran, scater, scRNAseq
SystemRequirements C++11
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package batchelor_1.5.5.tar.gz
Windows Binary batchelor_1.5.5.zip
macOS 10.13 (High Sierra) batchelor_1.5.5.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

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