Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.
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R Merge branch 'master' of github.com:saezlab/CellNOptR Mar 9, 2018
data
inst updated changelog and news Jan 11, 2018
man package manual updated Jan 11, 2018
src the solution of moving average issue pulled from permaCue branch Jul 12, 2018
tests mv files around Nov 12, 2014
vignettes cleaning up for Bioconductor Jan 10, 2018
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ChangeLog updated changelog and news Jan 11, 2018
DESCRIPTION updated changelog and news Jan 11, 2018
NAMESPACE
Readme.md installation instructions added to readme Apr 18, 2018

Readme.md

CellNOptR

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 <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/CellNOptR’)

Standard installation from Bioconductor

To install CellNOptR, type:

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

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

   biocLite("CNORdt")
   biocLite("CNORfeeder")
   biocLite("CNORfuzzy")
   biocLite("CNORode")

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".