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CARNIVAL

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

Bioconductor version: Release (3.17)

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 uni-heidelberg.de>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

BiocManager::install("CARNIVAL")

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("CARNIVAL")
Contextualizing large scale signalling networks from expression footprints with CARNIVAL HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Network, Software, Transcriptomics
Version 2.10.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0)
Imports readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown
Linking To
Suggests RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo
System Requirements
Enhances
URL https://github.com/saezlab/CARNIVAL
Bug Reports https://github.com/saezlab/CARNIVAL/issues
See More
Depends On Me
Imports Me cosmosR
Suggests Me dce
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CARNIVAL_2.10.0.tar.gz
Windows Binary CARNIVAL_2.10.0.zip (64-bit only)
macOS Binary (x86_64) CARNIVAL_2.10.0.tgz
macOS Binary (arm64) CARNIVAL_2.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CARNIVAL
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CARNIVAL
Bioc Package Browser https://code.bioconductor.org/browse/CARNIVAL/
Package Short Url https://bioconductor.org/packages/CARNIVAL/
Package Downloads Report Download Stats