lipi12q / cmapM

Connectivity Map analysis in MATLAB

cmapM: Connectivity Map Analysis in MATLAB®

Copyright (c) 2017, Connectivity Map (CMap) at the Broad Institute. All rights reserved.

Introduction

cmapM is a collection of MATLAB routines for analyzing data from the Connectivity Map project and made available under the free 3-clause BSD license.

Initial setup

After cloning the cmapM github repo. Change to the cmapM folder and run the following from the Matlab command window to setup environment variables, add cmapM to the Matlab search path, and download asset files:

setup_env

Contents

• Working with CMap data formats
• L1000 data-processing pipeline

Software Requirements

1. Matlab R2014b and above
2. Statistics Toolbox
3. Parallel Processing Toolbox [Optional]

Contributions

Bug reports, fixes and pull requests are welcome.