BatChef
This is the released version of BatChef; for the devel version, see BatChef.
Single-cell RNA-seq batch effects correction methods interface
Bioconductor version: Release (3.23)
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.
Author: Elena Zuin [aut, cre] (ORCID:
, 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)
Maintainer: Elena Zuin <elena.zuin.3 at phd.unipd.it>
citation("BatChef")):
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("BatChef")
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("BatChef")| BatChef vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Sequencing, SingleCell, Software |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL (>= 3) |
| 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 |
| System Requirements | |
| URL | https://github.com/zuinelena3/BatChef |
| Bug Reports | https://github.com/zuinelena3/BatChef/issues |
See More
| Suggests | BiocStyle, knitr, R.devices, rmarkdown, scater, testthat (>= 3.0.0) |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BatChef_1.0.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | BatChef_1.0.2.tgz |
| macOS Binary (sonoma-arm64) | BatChef_1.0.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BatChef |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BatChef |
| Bioc Package Browser | https://code.bioconductor.org/browse/BatChef/ |
| Package Short Url | https://bioconductor.org/packages/BatChef/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |