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

Bioconductor version: Release (3.19)

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.

Author: Enio Gjerga [aut] , Panuwat Trairatphisan [aut], Anika Liu [ctb], Alberto Valdeolivas [ctb], Nikolas Peschke [ctb], Aurelien Dugourd [ctb], Attila Gabor [cre], Olga Ivanova [aut]

Maintainer: Attila Gabor <attila.gabor at>

Citation (from within R, enter citation("CARNIVAL")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Contextualizing large scale signalling networks from expression footprints with CARNIVAL HTML R Script
Reference Manual PDF


biocViews GeneExpression, Network, Software, Transcriptomics
Version 2.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-3
Depends R (>= 4.0)
Imports readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown
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Suggests RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo
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Source Package CARNIVAL_2.14.0.tar.gz
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macOS Binary (x86_64) CARNIVAL_2.14.0.tgz
macOS Binary (arm64) CARNIVAL_2.14.0.tgz
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