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Connectivity Map analysis in MATLAB

License: BSD 3-Clause "New" or "Revised" License

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cmapm's Introduction

Preamble

This is a fork of cmap/cmapM to experiment with connectivity map analytics.

cmapM: Connectivity Map Analysis in MATLAB®

Introduction

cmapM is a library of of MATLAB® routines to process, analyze and visualize Connectivity Map (CMap) data. To learn more about the CMap project at the Broad Institute, please visit clue.io.

All code is made available under the free 3-clause BSD license.

Initial setup

Clone the cmapM code repository

git clone https://github.com/cmap/cmapM

Configure the MATLAB environment and download test datasets

% within a MATLAB sesssion type:
cd cmapM
setup

Documentation

Software Requirements

Matlab R2014b and above
Statistics Toolbox
Parallel Processing Toolbox [Optional]

Citation

If you find cmapM useful in your research, please cite: Subramanian, A. et al. A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Cell (2017)

If you use the GCTx annotated data matrix format in your work, please cite Enache et al.

Changelog

v2.0.0, Jan 4, 2021
- Added code and documentation for several Sigtools
- Added utility functions for L1000 data formats, algorithms and visualizations
- Updated documentation, tutorials and demo datasets
v1.0.2, Jun 28, 2017
- Fix for parse_gctx slicing issue #1
v1.0.1, May 6, 2017
- Refactored code from the now deprecated cmap/l1ktools
- Data and assets have been externalized to keep the repo size small
- Added Level 4 to Level 5 processing to L1000 data pipeline
v1.0.0, 2017
- Initial release