ARACNE-multicore

src/ARACNE.src.tar.gz -> Source code of ARACNe2.
parallel -> Python middleware scripts for run ARACNe2 on a platform multicore.
launch -> Dirctory to run ARACNe2 multicore.

Pre-requisites

python 3
pandas
multiprocessing
functools
os, sys

(Optional) Installing miniconda as bioconda

bash install-miniconda.sh

01 - Compiling ARACNe2

bash compile-aracne.sh

02 - Running ARACNe2 Multicore

Copy matrix gene expression into directory launch:

bash run.sh norm-Stage1.tsv &> salida &

For run multiple tsvs:

for i in $(ls *.tsv); do bash run.sh $i; done > salida &

03 - Random samples

To get a list of files with n samples randomized.

$ cd launch
$ mkdir Out
$ python randsamples.py

We considered file input is in folder launch. If you need change this input filename you can modify the code.

On Out directory is saved all files that you can copy to launch to run ARACne.

04 - miRNA (Optional)

To get only miRNA-gen interactions of a complete matrix of interactions. This script consider the name of files as *-compete.tsv and resolve all ocurences.

$ cd launch
$ python miRNA-gen.py

Output of this step is a directory called expr-miRNA with tsvs with miRNA-gen networks.