Combine Labs - RNA sequencing UI Tool

A web application for visualizing RNA sequencing results from the following tools/experiments

• Kallisto
• Sailfish
• RSEM

Tech Stack

• Python
• Flash Web Framework
• Scikit-Learn Library
• PostgreSQL Database
• Bootstrap UI
• Highcharts
• Bootstrap Data Tables

Getting Started

Python Installation

https://www.python.org/downloads/

Flask Installation

http://flask.pocoo.org/docs/0.10/installation/

scikit-learn Installation

http://scikit-learn.org/stable/install.html

PostgreSQL Installation

http://www.postgresql.org/download/

pg8000 python-postgreSQL driver

https://pypi.python.org/pypi/pg8000

Use the cb_psql_cmds.txt file to create database tables and import the experiment.

The code should be modified to point to the local database. This code change should be done in corecoeff.py and server.py.

Use the files in the scripts/ folder to convert, compute and store the results into the database.

• fasta_parser.py
• corelcoeff.py

Then start the server using

python server.py and visit http://localhost:5000 to visualize the dashboard