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CellNOptR ========= <!-- badges: start --> [![Lifecycle: stable](]( [![BioC status](]( <!-- badges: end --> Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data. - Please visit [CellNOptR]( for details about the project (references, news, ...) ## Installation: Before starting, make sure you have installed the latest version of R. For more information and download of R, please refer to [R project page]( . For more information about how to install R packages, please refer to [Installing packages]( ### Standard installation from Bioconductor To install CellNOptR, type: ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("CellNOptR", version = "3.8") ``` Then, you can also install other CellNOptR related packages:: ``` BiocManager::install("CNORdt") BiocManager::install("CNORfeeder") BiocManager::install("CNORfuzzy") BiocManager::install("CNORode") ``` ### Installation from GitHub Using the `devtools` package you can install the latest version from the GitHub repository: ``` if(!require("devtools")) install.packages("devtools") # installs devtools package if not already installed devtools::install_github("saezlab/CellNOptR", build_vignettes = TRUE) ``` To see the documentation of the package and a few examples, please type: ``` vignette("CellNOptR-vignette") ``` ### Install from a local copy of the package: install CellNOptR from a tar ball as follows: ``` install.packages("path_to_CellNOptR/CellNOptR_1.0.0.tar.gz", repos=NULL, type="source") ``` or, using the R GUI by clicking on "Packages & Data" then "Package installer", then choosing "local source" from the dropdown menu, clicking "install", choosing CellNOptR.1.0.0.tar.gz and finally clicking "open". ## Feedbacks, bug reports, features Feedbacks and bugreports are always very welcomed! Please use the Github issue page to report bugs or for questions: Many thanks! ## Code of Conduct Please note that the CellNOptR project is released with a [Contributor Code of Conduct]( By contributing to this project, you agree to abide by its terms.