CARNIVAL

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

Bioconductor version: 3.23 · Package version: 2.22.0

An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs' weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.

Installation

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

BiocManager::install("CARNIVAL")

Details

Maintainer	Attila Gabor <attila.gabor@uni-heidelberg.de>
Author	Enio Gjerga [aut] (ORCID: <https://orcid.org/0000-0002-3060-5786>), Panuwat Trairatphisan [aut], Anika Liu [ctb], Alberto Valdeolivas [ctb], Nikolas Peschke [ctb], Aurelien Dugourd [ctb], Attila Gabor [cre], Olga Ivanova [aut]
License	GPL-3
URL	https://github.com/saezlab/CARNIVAL
Bug Reports	https://github.com/saezlab/CARNIVAL/issues
Downloads rank	381
Source branch	RELEASE_3_23
biocViews	GeneExpression, Network, Software, Transcriptomics

Documentation

Contextualizing large scale signalling networks from expression footprints with CARNIVAL

Download

Source package

Dependencies

Depends: R (>= 4.0)

Imports: readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown

Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo

Reverse dependencies

Imports Me (1): cosmosR