Package: pareg
Title: Pathway enrichment using a regularized regression approach
Version: 1.8.0
Authors@R: 
    c(
        person(
            given = "Kim Philipp", family = "Jablonski",
            role = c("aut", "cre"),
            email = "kim.philipp.jablonski@gmail.com",
            comment = c(ORCID = "0000-0002-4166-4343")
        )
    )
Description: Compute pathway enrichment scores while accounting for term-term relations.
    This package uses a regularized multiple linear regression to regress differential expression p-values obtained from multi-condition experiments on a pathway membership matrix.
    By doing so, it is able to incorporate additional biological knowledge into the enrichment analysis and to estimate pathway enrichment scores more robustly.
URL: https://github.com/cbg-ethz/pareg
BugReports: https://github.com/cbg-ethz/pareg/issues
biocViews: Software, StatisticalMethod, GraphAndNetwork, Regression,
        GeneExpression, DifferentialExpression, NetworkEnrichment,
        Network
License: GPL-3
Encoding: UTF-8
LazyData: false
Depends: R (>= 4.2), tensorflow (>= 2.2.0), tfprobability (>= 0.10.0)
Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR,
        plotROC, PRROC, mgsa, topGO, msigdbr, betareg, fgsea,
        ComplexHeatmap, GGally, ggsignif, circlize, enrichplot,
        ggnewscale, tidyverse, cowplot, ggfittext, simplifyEnrichment,
        GSEABenchmarkeR, BiocParallel, ggupset, latex2exp,
        org.Hs.eg.db, GO.db
VignetteBuilder: knitr
RoxygenNote: 7.2.3
Imports: stats, tidyr, purrr, future, doFuture, foreach, doRNG, tibble,
        glue, tidygraph, igraph, proxy, dplyr, magrittr, ggplot2,
        ggraph, rlang, progress, Matrix, keras, nloptr, ggrepel,
        methods, DOSE, stringr, reticulate, logger, hms, devtools,
        basilisk
StagedInstall: no
git_url: https://git.bioconductor.org/packages/pareg
git_branch: RELEASE_3_19
git_last_commit: 8352b08
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-02 00:55:55 UTC; biocbuild
Author: Kim Philipp Jablonski [aut, cre]
    (<https://orcid.org/0000-0002-4166-4343>)
Maintainer: Kim Philipp Jablonski <kim.philipp.jablonski@gmail.com>
Built: R 4.4.0; ; 2024-05-02 13:15:34 UTC; windows
