Package: BatChef
Type: Package
Title: Single-cell RNA-seq batch effects correction methods interface
Version: 1.1.1
Authors@R: c(
    person("Elena", "Zuin", email = "elena.zuin.3@phd.unipd.it", 
            role = c("aut", "cre"),
            comment = c(ORCID = "0009-0006-3060-4835", 
            affiliation = "Department of Biology, University of Padova")),
    person("Chiara", "Romualdi", role = "ctb", 
            comment = c(affiliation = "Department of Biology, University of Padova")),
    person("Davide", "Risso", role = "ctb",
            comment = c(affiliation = "Department of Statistical Sciences, University of Padova")),
    person("Gabriele", "Sales", role = "ctb", 
            comment = c(affiliation = "Department of Biology, University of Padova")))
Description: 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.
Depends: R (>= 4.5.0)
License: GPL (>= 3)
Encoding: UTF-8
biocViews: BatchEffect, SingleCell, Sequencing
LinkingTo: Rcpp, RcppArmadillo
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
BugReports: https://github.com/zuinelena3/BatChef/issues
URL: https://github.com/zuinelena3/BatChef
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, R.devices, rmarkdown, scater, testthat (>=
        3.0.0)
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libabsl-dev libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libgdal-dev gdal-bin
        libgeos-dev git libglpk-dev make libharfbuzz-dev libhdf5-dev
        libicu-dev libjpeg-dev libpng-dev libtiff-dev libuv1-dev
        libwebp-dev libxml2-dev libssl-dev patch libproj-dev python3
        libsqlite3-dev libudunits2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-26 09:54:24 UTC
RemoteUrl: https://github.com/bioc/BatChef
RemoteRef: HEAD
RemoteSha: f3094973f99772ce6bf11417c466963bc17f918b
NeedsCompilation: yes
Packaged: 2026-06-26 10:30:41 UTC; root
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)
Maintainer: Elena Zuin <elena.zuin.3@phd.unipd.it>