Package: deconvR
Title: Simulation and Deconvolution of Omic Profiles
Version: 1.17.0
Date: 2025-07-28
Authors@R: 
    c(person(given = "Irem B.",
           family = "Gündüz",
           role = c("aut", "cre"),
           email = "irembgunduz@gmail.com",
           comment = c(ORCID = "0000-0003-2641-0916")),
      person(given = "Veronika",
           family = "Ebenal",
           role = c("aut"),
           email = "veronikaebenal@gmail.com",
           comment = c(ORCID = "0000-0001-7976-3964")),
      person(given = "Altuna",
           family = "Akalin",
           role = c("aut"),
           email = "aakalin@gmail.com",
           comment = c(ORCID = "0000-0002-0468-0117")))
Description: This package provides a collection of functions designed for 
      analyzing deconvolution of the bulk sample(s) using an atlas of reference 
      omic signature profiles and a user-selected model. Users are given the 
      option to create or extend a reference atlas and,also simulate the desired
      size of the bulk signature profile of the reference cell types.The package
      includes the cell-type-specific methylation atlas and, Illumina Epic B5 
      probe ids that can be used in deconvolution. Additionally,we included 
      BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.
License: Artistic-2.0
URL: https://github.com/BIMSBbioinfo/deconvR
BugReports: https://support.bioconductor.org/t/deconvR
biocViews: DNAMethylation, Regression, GeneExpression, RNASeq, SingleCell, 
    StatisticalMethod, Transcriptomics
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
Depends: 
    R (>= 4.1),
    data.table (>= 1.14.0)
Imports:
    S4Vectors (>= 0.30.0),
    methylKit (>= 1.18.0),
    IRanges (>= 2.26.0),
    GenomicRanges (>= 1.44.0),
    BiocGenerics (>= 0.38.0),
    stats,
    methods,
    foreach (>= 1.5.1),
    magrittr (>= 2.0.1),
    matrixStats (>= 0.61.0),
    e1071 (>= 1.7.9),
    quadprog (>= 1.5.8),
    nnls (>= 1.4),
    rsq (>= 2.2),
    MASS,
    utils,
    dplyr (>= 1.0.7),
    tidyr (>= 1.1.3),
    assertthat,
    minfi
Suggests: 
    testthat (>= 3.0.0),
    roxygen2 (>= 7.1.2),
    doParallel (>= 1.0.16),
    parallel,
    knitr (>= 1.34),
    BiocStyle (>= 2.20.2),
    reshape2 (>= 1.4.4),
    ggplot2 (>= 3.3.5),
    rmarkdown,
    devtools (>= 2.4.2),
    sessioninfo (>= 1.1.1),
    covr,
    granulator,
    RefManageR
VignetteBuilder: knitr
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/deconvR
git_branch: devel
git_last_commit: 25b6419
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
