CARNIVAL
This package is for version 3.12 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: 3.12
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>
citation("CARNIVAL")):
Installation
To install this package, start R (version "4.0") 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")| narray Usage Examples | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | GeneExpression, Network, Software, Transcriptomics |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | Apache License (== 3.0) | file LICENSE |
| Depends | R (>= 4.0) |
| Imports | doParallel, readr, viper, AnnotationDbi, Category, ggplot2, UniProt.ws, lpSolve, igraph |
| System Requirements | |
| URL | https://github.com/saezlab/CARNIVAL |
| Bug Reports | https://github.com/saezlab/CARNIVAL/issues |
See More
| Suggests | knitr, readxl, testthat (>= 2.1.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CARNIVAL_1.2.0.tar.gz |
| Windows Binary | CARNIVAL_1.2.0.zip |
| macOS 10.13 (High Sierra) | CARNIVAL_1.2.0.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 |
| Old Source Packages for BioC 3.12 | Source Archive |