CellNOptR
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CellNOptR.
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
Bioconductor version: 3.9
This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.
Author: T.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve
Maintainer: A.Gabor <gabor.attila87 at gmail.com>
citation("CellNOptR")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CellNOptR")
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("CellNOptR")| CellNOptR0_1flowchart.pdf | ||
| Fig2.pdf | ||
| Fig3.pdf | ||
| Fig4.pdf | ||
| Fig6.pdf | ||
| Fig7.pdf | ||
| Fig8.pdf | ||
| Main vignette:Playing with networks using CellNOptR | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bioinformatics, CellBasedAssays, CellBiology, ImmunoOncology, Proteomics, Software, TimeCourse |
| Version | 1.30.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (12.5 years) |
| License | GPL-3 |
| Depends | R (>= 2.15.0), RBGL, graph, methods, hash, RCurl, Rgraphviz, XML, ggplot2 |
| Imports | igraph, stringi, stringr |
| System Requirements | Graphviz version >= 2.2 |
| URL |
See More
| Suggests | data.table, plyr, dplyr, tidyr, readr, RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | CNORdt, CNORfeeder, CNORfuzzy, CNORode |
| Imports Me | |
| Suggests Me | MEIGOR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CellNOptR_1.30.0.tar.gz |
| Windows Binary | CellNOptR_1.30.0.zip |
| Mac OS X 10.11 (El Capitan) | CellNOptR_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CellNOptR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CellNOptR |
| Bioc Package Browser | https://code.bioconductor.org/browse/CellNOptR/ |
| Package Short Url | https://bioconductor.org/packages/CellNOptR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |