batchelor

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see batchelor.

Single-Cell Batch Correction Methods

Bioconductor version: 3.21

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 "4.5") 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 1.24.0

In Bioconductor since BioC 3.9 (R-3.6) (6.5 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.advanced, OSCA.intro, OSCA.multisample, OSCA.workflows

Imports Me chevreulProcess, ChromSCape, mumosa, scMerge, singleCellTK, scPipeline

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_1.24.0.tar.gz

Windows Binary (x86_64) batchelor_1.24.0.zip (64-bit only)

macOS Binary (x86_64) batchelor_1.24.0.tgz

macOS Binary (arm64) batchelor_1.24.0.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/

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