BatChef
Single-cell RNA-seq batch effects correction methods interface
Bioconductor version: 3.23 · Package version: 1.0.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
This package implements a variety of methods for batch correction in single-cell RNA sequencing (scRNA-seq) data. It incorporates quantitative metrics (e.g. Wasserstein distance, Adjusted Rand Index) to evaluate their performance. Furthermore, the package assists users in identifying and applying the optimal method for specific datasets.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BatChef")Details
| Maintainer | Elena Zuin <elena.zuin.3@phd.unipd.it> |
| Author | Elena Zuin [aut, cre] (ORCID: <https://orcid.org/0009-0006-3060-4835>, affiliation: Department of Biology, University of Padova), Chiara Romualdi [ctb] (affiliation: Department of Biology, University of Padova), Davide Risso [ctb] (affiliation: Department of Statistical Sciences, University of Padova), Gabriele Sales [ctb] (affiliation: Department of Biology, University of Padova) |
| License | GPL (>= 3) |
| URL | https://github.com/zuinelena3/BatChef |
| Bug Reports | https://github.com/zuinelena3/BatChef/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | BatchEffect, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/BatChef/ |
Citation
From within R, enter citation("BatChef"):
Elena Zuin. BatChef: Single-cell RNA-seq batch effects correction methods interface. doi:10.18129/B9.bioc.BatChef, R package version 1.0.2, https://bioconductor.org/packages/BatChef.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | BatChef_1.0.2.tar.gz |
| macOS binary (arm64) | BatChef_1.0.2.tgz |
| macOS binary (x86_64) | BatChef_1.0.2.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: anndata, aricode, batchelor, bluster, cluster, e1071, fitdistrplus, ggplot2, harmony, leidenAlg, limma, Matrix, mclust, methods, parallel, purrr, RANN, Rcpp, reticulate, rliger, S4Vectors, scCustomize, scMerge, scrapper, Seurat, SeuratObject, sf, SingleCellExperiment, SparseArray, splatter, stats, SummarizedExperiment, sva, transport, zellkonverter
LinkingTo: Rcpp, RcppArmadillo
Suggests: BiocStyle, knitr, R.devices, rmarkdown, scater, testthat (>= 3.0.0)