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
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:15:21 UTC
RemoteUrl: https://github.com/bioc/xcore
RemoteRef: HEAD
RemoteSha: a7dbfb4eaa16d0c6f5793d1c433d2ee46ecc8513
NeedsCompilation: no
Packaged: 2026-02-21 06:57:22 UTC; root
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; ; 2026-02-21 06:59:22 UTC; windows
