MechRNA
Source Code

MechRNA

MechRNA is a computational tool for integration RNA-RNA interactions, RNA-Protein interactions and correlation data in order to infer potential mechanisms for a lncRNA of interest.

How do I install MechRNA?

  1. Ensure you have the required dependancies:

    • IntaRNA2 >= 2.2.0
    • Python (tested with version 2.7 and 3.5) with packages:
      • numpy
      • scipy
      • statsmodels
      • configparser (Python2 only)

  2. Clone or download MechRNA:

     git clone https://bitbucket.org/compbio/mechrna.git

  3. Download the required data into /mechrna/data/ which can found here. The file structure should be as shown below:

     /mechrna/data/
 /mechrna/data/correlation/
 /mechrna/data/peaks/
 /mechrna/data/refs/

    For screening mode, please also download the correlation file for your cancer type of interest. This file should be placed in the /mechrna/data/correlations/ folder.

How do I run MechRNA?

You can use

python mechrna.py -h

to get a description of each parameter. For more details, please check doc/MechRNA_manual.pdf (coming soon).

To create a new hypothesis-driven mode project: specify (1) project name and (2) lncRNA transcript ID (3) Files listing the targets, rbps, and mechanisms you are intested in (all are used if not specified):

python mechrna.py -p my_project -l ENSTXXXXXXXXXXX -a [-T my_targets] [-B my_rbps] [-M my_mechanisms]

To create a new screening mode project: specify (1) project name and (2) lncRNA transcript ID (3) correlation file:

python mechrna.py -p my_project -l ENSTXXXXXXXXXXX -c ./data/correlation/correl.genenet.[cancer_type].tcga

The hypothesis-driven mode parameters can also be specified for screening mode. Screening mode is computationally expensive and should be executed with multiple workers [–num-worker] and ideally on a cluster [–mode slurm/sge/pbs].

Feel free to change my_project to any name you want. The TSV file with the prediction results will be generated in my_project.

Example run with lncRNA 7SL

This is the validation case from Gawronski et. al (DOI: 10.1093/bioinformatics/bty208)

To run MechRNA on this lncRNA, type the following when in the mechrna root directory:

python mechrna.py -p my_project -l ENST00000618786 -a -T ./example/7SL.ids -M ./example/7SL.mechs

Contact & Support

Feel free to drop any inquiry to agawrons at sfu dot ca.