CellNOptR
This is the development version of CellNOptR; for the stable release version, see CellNOptR.
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
Bioconductor version: Development (3.24)
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: Thomas Cokelaer [aut], Federica Eduati [aut], Aidan MacNamara [aut], S Schrier [ctb], Camille Terfve [aut], Enio Gjerga [ctb], Attila Gabor [cre]
Maintainer: Attila Gabor <attila.gabor at uni-heidelberg.de>
citation("CellNOptR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data with CellNOptR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, CellBiology, ImmunoOncology, Network, Pathways, Proteomics, Software, TimeCourse |
| Version | 1.59.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (15 years) |
| License | GPL-3 |
| Depends | R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown |
| Imports | igraph, stringi, stringr |
| System Requirements | Graphviz version >= 2.2 |
| URL |
See More
| Suggests | data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics |
| Linking To | |
| Enhances | doParallel, foreach |
| Depends On Me | CNORdt, CNORfuzzy, CNORode |
| Imports Me | bnem, CNORfeeder |
| 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_1.59.0.tar.gz |
| Windows Binary (x86_64) | CellNOptR_1.59.0.zip |
| macOS Binary (big-sur-x86_64) | CellNOptR_1.59.0.tgz |
| macOS Binary (sonoma-arm64) | CellNOptR_1.59.0.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 |