dce

This is the released version of dce; for the devel version, see dce.

Pathway Enrichment Based on Differential Causal Effects

Bioconductor version: Release (3.20)

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 "4.4") and enter:


if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Regression, Software, StatisticalMethod
Version	1.13.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 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
System Requirements
URL	https://github.com/cbg-ethz/dce
Bug Reports	https://github.com/cbg-ethz/dce/issues

Suggests	knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	dce_1.13.0.tar.gz
Windows Binary (x86_64)	dce_1.13.0.zip
macOS Binary (x86_64)	dce_1.13.0.tgz
macOS Binary (arm64)	dce_1.13.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/dce
Source Repository (Developer Access)	git clone [email protected]:packages/dce
Bioc Package Browser	https://code.bioconductor.org/browse/dce/
Package Short Url	https://bioconductor.org/packages/dce/
Package Downloads Report	Download Stats