Regulatory Network Workflow

This is a project to centralize the Workflow for the Computational Systems Biology/Integrative Genomics research group at INMEGEN in order to reproduce fully or partially previous analysis in new datasets.

For clone this repository and his submodules:

git clone https://github.com/CSB-IG/rnw.git
cd rnw/
git submodule init
git submodule update

1. Download data (implementation pending)

some attempts to automate the downloading of public data.

2. Data normalization/preprocessing

Tips and strategies for the preprocessing of genomic expression data.

###➔ Pathifier Miguel Angel García-Campos Pathifier enritchment tool kit:
https://github.com/AngelCampos/Pathifier-Tool-Kit

3. Network Generation

CSB-IG group HTCondor implementation for parallelize ARACNe's MI calculation:

https://github.com/CSB-IG/parallel-aracne

Diana Drago García tool kit for to take the parallel aracne output files in to minet to process regulatory networks (eg DPI implementation)

https://github.com/CSB-IG/miRNAseq_rnw

4. Subsequent spells:

###➔ INFOMAP Sergio Antonio Alcalá Corona convert a SIF like file to a Pajek like file ready to INFOMAP: https://github.com/saac/ComplexNetworks-ToolBox

The INFOMAP output can be analysed with Sergio Antonio Alcalá Corona's enritchment tool kit: https://github.com/saac/Enrichmentator

###➔ Transcriptional Master Regulators search (unfinished) Hugo Tovar's MARINa tool kit take the TF interactions from ARACNe networks and implement a TMRs search with ssmarina:

https://github.com/CSB-IG/tmr_search