dce
This is the development version of dce; for the stable release version, see dce.
Pathway Enrichment Based on Differential Causal Effects
DOI: 10.18129/B9.bioc.dce
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Kim Philipp Jablonski <kim.philipp.jablonski at gmail.com>
citation("dce")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
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 |
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_1.13.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |