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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 (3.19)

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 uni-heidelberg.de>

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

Installation

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


if (!require("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")
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 2.13.0
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
System Requirements
URL https://github.com/saezlab/CARNIVAL
Bug Reports https://github.com/saezlab/CARNIVAL/issues
See More
Suggests RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo
Linking To
Enhances
Depends On Me
Imports Me cosmosR
Suggests Me dce
Links To Me
Build Report Build Report

Package Archives

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

Source Package CARNIVAL_2.13.0.tar.gz
Windows Binary CARNIVAL_2.13.0.zip (64-bit only)
macOS Binary (x86_64) CARNIVAL_2.13.0.tgz
macOS Binary (arm64) CARNIVAL_2.13.0.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