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Welcome to the epigenetics-software wiki!

DaVie Epigenetics database:

• Quickstart Guide
• Loading data at the command line.

A demo version of the methylation component of the project can be found at http://echelon.cmmt.ubc.ca/dbaccess/ and may be tested using login "guest" and password "guest". This demonstration uses GEO sourced data.

This is a nascent project that will include several tools for epigenetics work:

Functioning Projects:

• A Database for storing epigenetic information
• A serverside interface called DaVIE for interrogating the database on a local server.
• A [walkthrough example](wiki/Walkthrough Example) for importing and analyzing methylation data.
• A walkthrough example for importing and analyzing chipseq data.
• Detailed explanation of [import scripts](wiki/Import DNA Methylation Data into Mongo), [analysis scripts](wiki/Analyzing Data from Mongo), illustration scripts and utility scripts.

Work in progress:

• WaveGenerator: a "peak caller" for chip-seq and other distribution based epigenetic marks that will provide reduced representation values for genomic coverage modelled after read distributions.

Please feel free to join this project or to check it out.

git clone https://github.com/apfejes/epigenetics-software.git

Requirements:

You will need to install the following packages to use this project.

• pysam
• scipy
• matplotlib
• pymongo
• django
• pyjade
• svgwrite
• keyring
• mongoengine
• django-nonrel
• djangotoolbox

To install these on a linux/debian/ubuntu system, you can use the pip installer*:

sudo pip install numpy scipy pysam matplotlib pymongo django pyjade svgwrite keyring mongoengine

Installing Security on Mongodb:

pip install git+https://github.com/django-nonrel/django@nonrel-1.6-beta pip install git+https://github.com/django-nonrel/djangotoolbox pip install git+https://github.com/django-nonrel/mongodb-engine --upgrade pip install django-mongo-auth

in the django_server directory:

Once the settings for the project have been set in the settings.py file, you must initialize the database. This creates the user/authentication database on your mongo implementation. python manage.py syncdb

To use the (now defunct) Lims system, you will also require:

• Node.js/express
• Forever (sudo npm install forever) - see: http://blog.nodejitsu.com/keep-a-nodejs-server-up-with-forever
• passport (npm install passport-local) - see http://passportjs.org/guide/
• passport-local (npm install passport-local) then run: ~/git//nodejs$ node_modules/forever/bin/forever start node app.js

To install the import from R system for Rdata files (methylumi objects), you must all install rpy2. If you're on a Debian/Ubuntu system.

sudo apt-get install python-rpy2

• Note, matplotlib requires your system include several libraries before you can build it. See http://matplotlib.org/users/installing.html#build-requirements for more details
• Similarly, pycogent requires two libraries, SQLAlchemy and MySQL-python, before it can be used to query Ensembl. See http://pycogent.org/install.html for details - Pycogent is not currently in use for any of the above code, as it's in testing.

Contributors:

Current contributors to this project:

• Anthony Fejes

Past contributors to this project:

• Scott Brown
• Dan Fornika
• Jake Yeung
• Sarah Perez