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This is the development version of CARNIVAL; for the stable release version, see CARNIVAL.

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

Bioconductor version: Development (3.20)

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))

# The following initializes usage of Bioc devel


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 2.15.0
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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Imports Me cosmosR
Suggests Me dce
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Source Package CARNIVAL_2.15.0.tar.gz
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macOS Binary (x86_64) CARNIVAL_2.15.0.tgz
macOS Binary (arm64) CARNIVAL_2.15.0.tgz
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