Pathway Enrichment Based on Differential Causal Effects

Bioconductor version: Release (3.19)

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.

Author: Kim Philipp Jablonski [aut, cre] , Martin Pirkl [aut]

Maintainer: Kim Philipp Jablonski <kim.philipp.jablonski at gmail.com>

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biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Regression, Software, StatisticalMethod
Version 1.12.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 4.1)
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
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URL https://github.com/cbg-ethz/dce
Bug Reports https://github.com/cbg-ethz/dce/issues
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Suggests knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL
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Source Package dce_1.12.0.tar.gz
Windows Binary dce_1.12.0.zip
macOS Binary (x86_64) dce_1.12.0.tgz
macOS Binary (arm64) dce_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/dce
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/dce
Bioc Package Browser https://code.bioconductor.org/browse/dce/
Package Short Url https://bioconductor.org/packages/dce/
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