DOI: 10.18129/B9.bioc.batchelor  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see batchelor.

Single-Cell Batch Correction Methods

Bioconductor version: 3.16

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>

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HTML R Script 1. Correcting batch effects
HTML R Script 2. Extending methods
PDF   Reference Manual
Text   NEWS


biocViews BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.14.1
In Bioconductor since BioC 3.9 (R-3.6) (4 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
LinkingTo Rcpp
Suggests testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq
SystemRequirements C++11
Depends On Me OSCA.advanced, OSCA.intro, OSCA.multisample, OSCA.workflows
Imports Me ChromSCape, mumosa, singleCellTK
Suggests Me TSCAN
Links To Me
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