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cmapM: Connectivity Map Analysis in MATLAB®

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


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

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

Initial setup

  • Clone the cmapM code repository
git clone
  • Configure the MATLAB environment and download test datasets
% within a MATLAB sesssion type:
cd cmapM


Software Requirements

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


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.


  • 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


Bug reports, fixes and pull requests are welcome.