Package: dce
Type: Package
Title: Pathway Enrichment Based on Differential Causal Effects
Version: 1.12.0
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")
        ),
        person(
            given = "Martin", family = "Pirkl",
            role = c("aut"),
            email = "martinpirkl@yahoo.de"
        )
    )
Description: Compute differential causal effects (dce) on (biological) networks.
    Given observational samples from a control experiment and non-control (e.g., cancer) for two genes A and B, we can compute differential causal effects with a (generalized) linear regression.
    If the causal effect of gene A on gene B in the control samples is different from the causal effect in the non-control samples the dce will differ from zero.
    We regularize the dce computation by the inclusion of prior network information from pathway databases such as KEGG.
URL: https://github.com/cbg-ethz/dce
BugReports: https://github.com/cbg-ethz/dce/issues
biocViews: Software, StatisticalMethod, GraphAndNetwork, Regression,
        GeneExpression, DifferentialExpression, NetworkEnrichment,
        Network, KEGG
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1)
Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR,
        cowplot, ggplotify, dagitty, lmtest, sandwich, devtools,
        curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel,
        docopt, CARNIVAL
VignetteBuilder: knitr
RoxygenNote: 7.1.2
Imports: stats, methods, assertthat, graph, pcalg, purrr, tidyverse,
        Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS, edgeR,
        epiNEM, igraph, metap, mnem, naturalsort, ppcor, glm2,
        graphite, reshape2, dplyr, magrittr, glue, Rgraphviz,
        harmonicmeanp, org.Hs.eg.db, logger, shadowtext
git_url: https://git.bioconductor.org/packages/dce
git_branch: RELEASE_3_19
git_last_commit: 28e0453
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-01 22:22:26 UTC; biocbuild
Author: Kim Philipp Jablonski [aut, cre]
    (<https://orcid.org/0000-0002-4166-4343>),
  Martin Pirkl [aut]
Maintainer: Kim Philipp Jablonski <kim.philipp.jablonski@gmail.com>
Built: R 4.4.0; ; 2024-05-02 12:41:15 UTC; windows
