batchelor
This is thereleased version of batchelor; for the devel version, seebatchelor.
Single-Cell Batch Correction Methods
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("batchelor")For older versions of R, please refer to the appropriateBioconductor 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 | 1.26.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (6.5 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 | chevreulProcess,ChromSCape,mumosa,scMerge,singleCellTK,scPipeline |
| Suggests Me | anglemania,TSCAN,Canek,RaceID |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | batchelor_1.26.0.tar.gz |
| Windows Binary (x86_64) | batchelor_1.26.0.zip |
| macOS Binary (x86_64) | batchelor_1.26.0.tgz |
| macOS Binary (arm64) | batchelor_1.26.0.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 |