dce

DOI: 10.18129/B9.bioc.dce    

This is the development version of dce; for the stable release version, see dce.

Pathway Enrichment Based on Differential Causal Effects

Bioconductor version: Development (3.14)

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>

Citation (from within R, enter citation("dce")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("dce")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("dce")

 

HTML R Script Get started
HTML R Script Overview of pathway network databases
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Regression, Software, StatisticalMethod
Version 1.1.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License GPL-3
Depends R (>= 4.1)
Imports stats, methods, assertthat, graph, pcalg, purrr, tidyverse, Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS, CombinePValue, edgeR, epiNEM, igraph, metap, mnem, naturalsort, ppcor, glm2, graphite, reshape2, dplyr, glue, Rgraphviz, harmonicmeanp, org.Hs.eg.db, logger
LinkingTo
Suggests knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment
SystemRequirements
Enhances
URL https://github.com/cbg-ethz/dce
BugReports https://github.com/cbg-ethz/dce/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package dce_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) dce_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/dce
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/dce
Package Short Url https://bioconductor.org/packages/dce/
Package Downloads Report Download Stats

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