Package: xcore
Title: xcore expression regulators inference
Version: 1.15.0
Authors@R: 
    c(person(given = "Maciej",
           family = "Migdał",
           role = c("aut", "cre"),
           email = "mcjmigdal@gmail.com",
           comment = c(ORCID = "0000-0002-8021-7263")),
      person(given = "Bogumił",
           family = "Kaczkowski",
           role = c("aut"),
           email = "mcjmigdal@gmail.com",
           comment = c(ORCID = "0000-0001-6554-5608"))
     )
Description: xcore is an R package for transcription factor activity modeling
  based on known molecular signatures and user's gene expression data.
  Accompanying xcoredata package provides a collection of molecular signatures,
  constructed from publicly available ChiP-seq experiments. xcore use ridge
  regression to model changes in expression as a linear combination of molecular
  signatures and find their unknown activities. Obtained, estimates can be further 
  tested for significance to select molecular signatures with the highest predicted 
  effect on the observed expression changes.
License: GPL-2
Encoding: UTF-8
LazyData: false
Depends: R (>= 4.2)
Imports: DelayedArray (>= 0.18.0), edgeR (>= 3.34.1), foreach (>=
        1.5.1), GenomicRanges (>= 1.44.0), glmnet (>= 4.1.2), IRanges
        (>= 2.26.0), iterators (>= 1.0.13), magrittr (>= 2.0.1), Matrix
        (>= 1.3.4), methods (>= 4.1.1), MultiAssayExperiment (>=
        1.18.0), stats, S4Vectors (>= 0.30.0), utils
Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0),
        BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>=
        1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16),
        ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>=
        1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>=
        2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis
        (>= 2.0.1), xcoredata
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Config/testthat/edition: 3
biocViews: GeneExpression, GeneRegulation, Epigenetics, Regression,
        Sequencing
git_url: https://git.bioconductor.org/packages/xcore
git_branch: devel
git_last_commit: a7dbfb4
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
Date/Publication: 2025-12-08
NeedsCompilation: no
Packaged: 2025-12-08 23:06:29 UTC; biocbuild
Author: Maciej Migdał [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-8021-7263>),
  Bogumił Kaczkowski [aut] (ORCID:
    <https://orcid.org/0000-0001-6554-5608>)
Maintainer: Maciej Migdał <mcjmigdal@gmail.com>
Built: R 4.6.0; ; 2025-12-09 04:53:05 UTC; unix
