Package: decontX
Title: Decontamination of single cell genomics data
Version: 1.8.0
Authors@R: 
    c(person("Yuan", "Yin", , "yuan_yin@outlook.com", role = c("aut"),
           comment = c(ORCID = "0000-0001-9261-6061")),
      person("Masanao", "Yajima", , "yajima@bu.edu", role = c("aut"),
           comment = c(ORCID = "0000-0002-7583-3707")),
      person("Joshua", "Campbell", , "camp@bu.edu", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-0780-8662")))
Description: This package contains implementation of DecontX (Yang et
        al. 2020), a decontamination algorithm for single-cell RNA-seq,
        and DecontPro (Yin et al. 2023), a decontamination algorithm
        for single cell protein expression data. DecontX is a novel
        Bayesian method to computationally estimate and remove RNA
        contamination in individual cells without empty droplet
        information. DecontPro is a Bayesian method that estimates the
        level of contamination from ambient and background sources in
        CITE-seq ADT dataset and decontaminate the dataset.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Suggests: BiocStyle, dplyr, knitr, rmarkdown, scran,
        SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports: celda, dbscan, DelayedArray, ggplot2, Matrix (>= 1.5.3),
        MCMCprecision, methods, patchwork, plyr, Rcpp (>= 0.12.0),
        RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1),
        rstantools (>= 2.2.0), S4Vectors, scater, Seurat,
        SingleCellExperiment, SummarizedExperiment, withr
Biarch: true
Depends: R (>= 4.3.0)
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0),
        RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>=
        2.18.0)
SystemRequirements: GNU make
VignetteBuilder: knitr
biocViews: SingleCell, Bayesian
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        libfribidi-dev libglpk-dev make libharfbuzz-dev libicu-dev
        libjpeg-dev libpng-dev libtiff-dev libwebp-dev libxml2-dev
        libssl-dev perl python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:26:26 UTC
RemoteUrl: https://github.com/bioc/decontX
RemoteRef: RELEASE_3_22
RemoteSha: e98b38cdfd6286b03c49d6c371a560de1d5ac451
NeedsCompilation: yes
Packaged: 2026-03-12 09:11:31 UTC; root
Author: Yuan Yin [aut] (ORCID: <https://orcid.org/0000-0001-9261-6061>),
  Masanao Yajima [aut] (ORCID: <https://orcid.org/0000-0002-7583-3707>),
  Joshua Campbell [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0780-8662>)
Maintainer: Joshua Campbell <camp@bu.edu>
Built: R 4.5.2; x86_64-w64-mingw32; 2026-03-12 09:15:38 UTC; windows
Archs: x64
