CARNIVAL

DOI: 10.18129/B9.bioc.CARNIVAL    

This package is for version 3.11 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: 3.11

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 <enio.gjerga at gmail.com> Panuwat Trairatphisan Anika Liu Alberto Valdeolivas Nikolas Peschke

Maintainer: Enio Gjerga <enio.gjerga at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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	narray Usage Examples
PDF		Reference Manual
Text		LICENSE

Details

biocViews	GeneExpression, Network, Software, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.11 (R-4.0) (0.5 years)
License	Apache License (== 3.0) | file LICENSE
Depends	R (>= 4.0)
Imports	doParallel, readr, viper, AnnotationDbi, Category, ggplot2, UniProt.ws, lpSolve, igraph
LinkingTo
Suggests	knitr, readxl, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL	https://github.com/saezlab/CARNIVAL
BugReports	https://github.com/saezlab/CARNIVAL/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CARNIVAL_1.0.0.tar.gz
Windows Binary	CARNIVAL_1.0.0.zip
macOS 10.13 (High Sierra)	CARNIVAL_1.0.0.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/
Package Downloads Report	Download Stats