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Martin Garrido Rodriguez-Cordoba edited this page Mar 30, 2020 · 4 revisions

MIGNON

Build Status

Mechanistic InteGrative aNalysis Of rNa-seq data

This repository contains all the necessary code to execute MIGNON, a bioinformatic workflow for the analysis of RNA-Seq data capable of integrating genomic and transcriptomic information into mechanistic signaling circuits. It covers the whole process using state-of-the-art tools and is deployable in under different computational environments. By using an in-silico knockdown strategy, it calculates the signaling circuit activities from gene expression and genomic variants using raw reads as input. It is written using the Workflow Description Language (WDL) and can be executed using Cromwell and Docker.

Dependencies

  1. Docker.
  2. Java (v1.8.0).
  3. Cromwell.

Quick Start

$ git clone https://github.com/babelomics/MIGNON.git
$ cd MIGNON
$ java -Dconfig.file=configs/LocalWithDocker.conf -jar /path/to/cromwell.jar run wdl/MIGNON.wdl /path/to/input.json

For more information about MIGNON, please visit the documentation.

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