CARNIVAL
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
Bioconductor version: Release (3.20)
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("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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Network, Software, Transcriptomics |
| Version | 2.16.0 |
| 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 |
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_2.16.0.tar.gz |
| Windows Binary (x86_64) | CARNIVAL_2.16.0.zip |
| macOS Binary (x86_64) | CARNIVAL_2.16.0.tgz |
| macOS Binary (arm64) | CARNIVAL_2.15.0.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 |