/shirloc

pipeline to identify ribosomal shifts of transcripts from polysome profiling rna-seq data.

Primary LanguagePython

ShiRlOc - Shifts in Ribosomal Occupancy

A computational pipeline to identify transcripts which shift in ribosomal occupancy between two conditions from Polysome Profiling RNA-Seq data.

Alt text Illustration by Faisal Mohammad

Hardware and Software Requirments

Download and Installation

# Download the latest release of shirloc using git
git clone https://github.com/warif2/shirloc.git

# Install python packages needed to run shirloc
pip install -r /shirloc/requirements.txt

QuickStart Guide

References

Shirloc is an ongoing project and will continue to improve on the methodology. Here is the paper that describes the experimental methods to perform polysome fractionation and subsequent RNA-Seq. If you use Shirloc, please cite these papers in your work!

Cell-type specific polysome profiling from mammalian tissues. Joe Seimetz, Waqar Arif, Sushant Bangru, Mikel Herneaz, Auinash Kalsotra. Methods, 2018, doi.org/10.1016/j.ymeth.2018.11.015.

Support

shirloc google group