BatChef
This is the development version of BatChef; to use it, please install the devel version of Bioconductor.
Single-cell RNA-seq batch effects correction methods interface
Bioconductor version: Development (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | BatchEffect, Sequencing, SingleCell, Software |
| Version | 0.99.12 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| 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_0.99.12.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | BatChef_0.99.12.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 |