CARNIVAL
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
Bioconductor version: 3.24 · Package version: 2.23.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CARNIVAL")Details
| Maintainer | Attila Gabor <attila.gabor@uni-heidelberg.de> |
| Author | Enio Gjerga [aut] (ORCID: <https://orcid.org/0000-0002-3060-5786>), Panuwat Trairatphisan [aut], Anika Liu [ctb], Alberto Valdeolivas [ctb], Nikolas Peschke [ctb], Aurelien Dugourd [ctb], Attila Gabor [cre], Olga Ivanova [aut] |
| License | GPL-3 |
| URL | https://github.com/saezlab/CARNIVAL |
| Bug Reports | https://github.com/saezlab/CARNIVAL/issues |
| Downloads rank | 517 |
| Source branch | devel |
| biocViews | GeneExpression, Network, Software, Transcriptomics |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | CARNIVAL_2.23.0.tar.gz |
| Windows binary (x86_64) | CARNIVAL_2.23.0.zip |
| macOS binary (arm64) | CARNIVAL_2.23.0.tgz |
| macOS binary (x86_64) | CARNIVAL_2.23.0.tgz |
Dependencies
Depends: R (>= 4.0)
Imports: readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown
Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo
Reverse dependencies
Imports Me (1): cosmosR