batchelor

DOI: 10.18129/B9.bioc.batchelor    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see batchelor.

Single-Cell Batch Correction Methods

Bioconductor version: 3.9

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 a simple sparsity-preserving translation of the population means. Functions are also provided for 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 different batches.

Author: Aaron Lun [aut, cre]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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

Details

biocViews	BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.0.1
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	GPL-3
Depends	SingleCellExperiment
Imports	SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, BiocNeighbors, BiocSingular, Matrix, DelayedArray, DelayedMatrixStats, scater, BiocParallel
LinkingTo	Rcpp, beachmat
Suggests	testthat, BiocStyle, knitr, beachmat, scRNAseq
SystemRequirements	C++11
Enhances
URL
Depends On Me
Imports Me
Suggests Me	simpleSingleCell
Links To Me
Build Report

Package Archives

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

Source Package	batchelor_1.0.1.tar.gz
Windows Binary	batchelor_1.0.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	batchelor_1.0.1.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