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cmapM
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Connectivity Map analysis in MATLAB
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cmapM
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# cmapM: Connectivity Map Analysis in MATLAB® Copyright (c) 2017, Connectivity Map (CMap) at the Broad Institute. All rights reserved. ## 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](https://clue.io). All code is made available under the free [3-clause BSD license](LICENSE.txt). ## Initial setup - Clone the cmapM code repository ```bash git clone https://github.com/cmap/cmapM ``` - Configure the MATLAB environment and download test datasets ```matlab % within a MATLAB sesssion type: cd cmapM setup ``` ## Documentation * [Working with CMap data formats](docs/Formats.md) * [L1000 data-processing pipeline](docs/DataPipeline.md) * [Running Connectivity Algorithms with SigTools](docs/SigToolDemo.md) ## Software Requirements 1. Matlab R2014b and above 2. Statistics Toolbox 3. 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)](https://doi.org/10.1016/j.cell.2017.10.049) If you use the GCTx annotated data matrix format in your work, please cite [Enache et al.](https://doi.org/10.1093/bioinformatics/bty784) ## Changelog - v2.0.0, Jan 4, 2021 - Added code and documentation for several [Sigtools](https://cmap.github.io/cmap-sig-tools) - 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 ## Contributing Bug reports, fixes and pull requests are welcome.
