CARNIVAL

DOI: 10.18129/B9.bioc.CARNIVAL    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	GeneExpression, Network, Software, Transcriptomics
Version	2.6.2
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	GPL-3
Depends	R (>= 4.0)
Imports	readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown
LinkingTo
Suggests	RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo
SystemRequirements
Enhances
URL	https://github.com/saezlab/CARNIVAL
BugReports	https://github.com/saezlab/CARNIVAL/issues
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_2.6.2.tar.gz
Windows Binary	CARNIVAL_2.6.2.zip
macOS Binary (x86_64)	CARNIVAL_2.6.2.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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive