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 (3.20)
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")
# 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 | ||
NEWS | Text |
Details
biocViews | GeneExpression, Network, Software, Transcriptomics |
Version | 2.15.0 |
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_2.15.0.tar.gz |
Windows Binary | CARNIVAL_2.15.0.zip |
macOS Binary (x86_64) | CARNIVAL_2.15.0.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 |