Bioconductor version: Release (3.15)
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")
):
To install this package, start R (version "4.2") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CARNIVAL")
HTML | R Script | Contextualizing large scale signalling networks from expression footprints with CARNIVAL |
Reference Manual | ||
Text | NEWS |
biocViews | GeneExpression, Network, Software, Transcriptomics |
Version | 2.6.2 |
In Bioconductor since | BioC 3.11 (R-4.0) (2.5 years) |
License | GPL-3 |
Depends | R (>= 4.0) |
Imports | readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown |
LinkingTo | |
Suggests | RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo |
SystemRequirements | |
Enhances | |
URL | https://github.com/saezlab/CARNIVAL |
BugReports | https://github.com/saezlab/CARNIVAL/issues |
Depends On Me | |
Imports Me | cosmosR |
Suggests Me | dce |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | CARNIVAL_2.6.2.tar.gz |
Windows Binary | CARNIVAL_2.6.2.zip |
macOS Binary (x86_64) | CARNIVAL_2.6.2.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 |
Old Source Packages for BioC 3.15 | Source Archive |
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