Readme.md

In saezlab/CNORdt: Add-on to CellNOptR: Discretized time treatments

CNORdt

CNORdt is an extension of CellNOptR that allows to train a Boolean model agains time-courses of data. Please visit the package on the Bioconductor page for further details or check http://www.cellnopt.org/ for a detailed description of CellNOptR.

Related tool: CNORode2017: train, simulate and predict with a continuous time logic based model

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 <http://www.r-project.org/> . For more information about how to install R packages, please refer to Installing package <http://cran.r-project.org/doc/manuals/R-admin.html#Installing-packages> These packages rely on several Bioconductor package (e.g., RBGL, graph, methods, etc.). As an example, you can install RGBL package by typing:

  source("http://bioconductor.org/biocLite.R")
  biocLite("RBGL")

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/CNORdt’)

Standard installation from Bioconductor

To install CNORdt, type:

  source("http://bioconductor.org/biocLite.R")
  biocLite("CNORdt")

Then, you can also install other CellNOptR related packages::

   biocLite("CellNOptR")
   biocLite("CNORfeeder")
   biocLite("CNORfuzzy")
   biocLite("CNORode")

Install from a local copy of the package:

install CNORdt from a tar ball as follows:

install.packages("path_to_CNORdt/CNORdt_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 CNORdt.1.0.0.tar.gz and finally clicking "open".

saezlab/CNORdt documentation built on May 17, 2019, 1:59 p.m.