batchelor
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see batchelor.
Single-Cell Batch Correction Methods
Bioconductor version: 3.13
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("batchelor")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.8.1 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 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 |
| System Requirements | C++11 |
| URL |
See More
| 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 | ChromSCape, mumosa, singleCellTK |
| Suggests Me | TSCAN |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | batchelor_1.8.1.tar.gz |
| Windows Binary | batchelor_1.8.1.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | batchelor_1.8.1.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |