Package: deconvR
Title: Simulation and Deconvolution of Omic Profiles
Version: 1.15.1
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: 120759a
git_last_commit_date: 2025-07-28
Repository: Bioconductor 3.22
Date/Publication: 2025-07-29
NeedsCompilation: no
Packaged: 2025-07-29 22:33:34 UTC; biocbuild
Author: Irem B. Gündüz [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2641-0916>),
  Veronika Ebenal [aut] (ORCID: <https://orcid.org/0000-0001-7976-3964>),
  Altuna Akalin [aut] (ORCID: <https://orcid.org/0000-0002-0468-0117>)
Maintainer: Irem B. Gündüz <irembgunduz@gmail.com>
Built: R 4.5.1; ; 2025-07-30 13:07:16 UTC; windows
