CARNIVAL

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see CARNIVAL.

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

Bioconductor version: 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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, Network, Software, Transcriptomics

Version 2.14.0

In Bioconductor since BioC 3.11 (R-4.0) (4.5 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

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

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Package Archives

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

Source Package CARNIVAL_2.14.0.tar.gz

Windows Binary (x86_64) CARNIVAL_2.14.0.zip

macOS Binary (x86_64) CARNIVAL_2.14.0.tgz

macOS Binary (arm64) CARNIVAL_2.14.0.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/

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