DOI: 10.18129/B9.bioc.batchelor    

Single-Cell Batch Correction Methods

Bioconductor version: Release (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>

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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 1.6.2
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
Suggests testthat, BiocStyle, knitr, scran, scater, bluster, scRNAseq
SystemRequirements C++11
Depends On Me
Imports Me ChromSCape, singleCellTK
Suggests Me TSCAN
Links To Me
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