CARNIVAL

DOI: 10.18129/B9.bioc.CARNIVAL    

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 (3.14)

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], Olga Ivanova [cre]

Maintainer: Olga Ivanova <olga.ivanova at bioquant.uni-heidelberg.de>

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

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, Network, Software, Transcriptomics
Version 2.3.0
In Bioconductor since BioC 3.11 (R-4.0) (1.5 years)
License GPL-3
Depends R (>= 4.0)
Imports readr, stringr, lpSolve, igraph, dplyr, rjson, rmarkdown, methods
LinkingTo
Suggests knitr, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL https://github.com/saezlab/CARNIVAL
BugReports https://github.com/saezlab/CARNIVAL/issues
Depends On Me
Imports Me cosmosR
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package CARNIVAL_2.3.0.tar.gz
Windows Binary CARNIVAL_2.3.0.zip
macOS 10.13 (High Sierra) CARNIVAL_2.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CARNIVAL
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CARNIVAL
Package Short Url https://bioconductor.org/packages/CARNIVAL/
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