batchelor

DOI: 10.18129/B9.bioc.batchelor    

Single-Cell Batch Correction Methods

Bioconductor version: Release (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>

Citation (from within R, enter citation("batchelor")):

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 http://bioconductor.org/packages/batchelor/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive

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