batchelor
This is the released version of batchelor; for the devel version, see batchelor.
Single-Cell Batch Correction Methods
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.28.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 years) |
| License | GPL-3 |
| Depends | SingleCellExperiment |
| Imports | SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, SparseArray, DelayedArray(>= 0.31.5), 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 | BatChef, chevreulProcess, ChromSCape, mumosa, scMerge, singleCellTK |
| Suggests Me | anglemania, TSCAN, Canek, RaceID |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | batchelor_1.28.0.tar.gz |
| Windows Binary (x86_64) | batchelor_1.28.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | batchelor_1.28.0.tgz |
| macOS Binary (sonoma-arm64) | batchelor_1.28.0.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 |