Package: pareg
Title: Pathway enrichment using a regularized regression approach
Version: 1.2.0
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,
        devtools, plotROC, PRROC, mgsa, topGO, msigdbr, betareg, fgsea,
        ComplexHeatmap, GGally, ggsignif, circlize, enrichplot,
        ggnewscale, tidyverse, cowplot, ggfittext
VignetteBuilder: knitr
RoxygenNote: 7.1.2
Imports: stats, tidyr, purrr, furrr, tibble, glue, tidygraph, igraph,
        proxy, dplyr, magrittr, ggplot2, ggraph, rlang, progress,
        Matrix, matrixLaplacian, keras, nloptr, shadowtext, methods,
        DOSE, stringr, reticulate
git_url: https://git.bioconductor.org/packages/pareg
git_branch: RELEASE_3_16
git_last_commit: 1b98e91
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-01
NeedsCompilation: no
Packaged: 2022-11-01 22:25:40 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 4.2.2; ; 2022-11-07 17:45:24 UTC; unix
