Welcome to the new bioconductor.org!

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 (3.19)

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>

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")

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

Details

biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Regression, Software, StatisticalMethod
Version 1.11.0
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
System Requirements
URL https://github.com/cbg-ethz/dce
Bug Reports https://github.com/cbg-ethz/dce/issues
See More
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_1.11.0.tar.gz
Windows Binary dce_1.11.0.zip
macOS Binary (x86_64) dce_1.11.0.tgz
macOS Binary (arm64) dce_1.11.0.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/
Package Downloads Report Download Stats