saezlab / cellnopt

Tool for training of logic models of signalling networks using prior knowledge networks and perturbation data.

CellNopt package collection

In support for the paper

Enio Gjerga, Panuwat Trairatphisan, Attila Gabor, Hermann Koch, Celine Chevalier, Franceco Ceccarelli, Aurelien Dugourd, Alexander Mitsos, Julio Saez-Rodriguez, Converting networks to predictive logic models from perturbation signalling data with CellNOpt, Bioinformatics, Volume 36, Issue 16, 15 August 2020, Pages 4523–4524, https://doi.org/10.1093/bioinformatics/btaa561

Packages:

CellNOptR: https://github.com/saezlab/CellNOptR

CNORode: https://github.com/saezlab/CNORode

CellNOpt-Feeder: https://github.com/saezlab/CellNOpt-Feeder

CNORProb: https://github.com/saezlab/CNORprob

CellNOpt-MaBoSS: https://github.com/saezlab/CellNOptR-MaBoSS

ShinyCNOR (Online): https://saezlab.shinyapps.io/shinycnor/

ShinyCNOR (GitHub): https://github.com/saezlab/ShinyCNOR

The CellNOoptR, CNORode and the CellNOpt-Feeder updates have also been implemented in Bioconductor and they can be respectively found in:

CellNOptR: https://www.bioconductor.org/packages/release/bioc/html/CellNOptR.html

CNORode: https://www.bioconductor.org/packages/release/bioc/html/CNORode.html

CNORfeeder: https://www.bioconductor.org/packages/release/bioc/html/CNORfeeder.html

License

Distributed under the GPLv3 License. See accompanying file LICENSE.txt or copy at: http://www.gnu.org/licenses/gpl-3.0.html

Website

CellNOpt website: http://www.cellnopt.org