dce

DOI: 10.18129/B9.bioc.dce    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see dce.

Pathway Enrichment Based on Differential Causal Effects

Bioconductor version: 3.13

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>

Installation

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

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

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	1.0.0
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_1.0.0.tar.gz
Windows Binary	dce_1.0.0.zip
macOS 10.13 (High Sierra)	dce_1.0.0.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