DESCRIPTION

Package: decontX
Title: Decontamination of single cell genomics data
Version: 1.0.0
Authors@R: 
    c(person("Yuan", "Yin", , "yuan_yin@outlook.com", role = c("aut", "cre"),
           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"),
           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: 7.2.3
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