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 (3.21)

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] (ORCID: ), 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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, Network, Software, Transcriptomics
Version	2.17.0
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
Build Report	Build Report

Package Archives

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

Source Package	CARNIVAL_2.17.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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