TGAC/MultiPEN

Name: MultiPEN

Owner: Earlham Institute

Description: null

Created: 2016-11-02 17:43:26.0

Updated: 2017-07-05 14:20:18.0

Pushed: 2017-07-11 09:06:20.0

Homepage: null

Size: 94045

Language: Matlab

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README

MultiPEN

MultiPEN is a tool for the analysis of multi-omics data. We are developing our first version which will include a tool to analyse transcriptomics and metabolomics data. We are extending an approach based on a regularised logistic regression model [1] that uses a biological network as a priori knowledge.

Using the Application

MultiPEN is shared as a MATLAB stand-alone application, which requires the installation of the MATLAB Runtime:

1. Download and save MATLAB Runtime for R2015b for your operating system here.

2. Double click the installer and follow the instructions in the installation wizard.

3. Download the application (v.0.0.1 to be released soon! - OS and Linux).

Running MultiPEN

Details on how to use MultiPEN can be found in the documentation.

Using the MATLAB code

To use the MATLAB code, install the required libraries:

1. Install TFCOS
2. Install the MATLAB gaimc package (to determine connected network components).
3. Download GenePEN [1]. (Note that in this work we use a slightly modified version of GenePEN. More details to be provided soon).

About Us

This repository is developed by the Jurkowski Group in the Earlham Institute. It is updated and maintained by Perla Rey, who can be reached by email on Perla.TroncosoRey@earlham.ac.uk

References

1. GenePEN: analysis of network activity alterations in complex diseases via the pairwise elastic net., Vlassis N, Glaab E., Stat Appl Genet Mol Biol. 2015 Apr;14(2):221-4. doi: 10.1515/sagmb-2014-0045.