Cell Maps CoEmbedding

The Cell Maps CoEmbedding is part of the Cell Mapping Toolkit

Creates Coembedding from Cell Maps ImmunoFluorscent Image Embedder and Cell Maps PPI Embedder using an implementation of MUSE or using the ProteinProjector co-embedding algorithm (formerly ProteinGPS).

• Free software: MIT license

• Source code: https://github.com/idekerlab/cellmaps_coembedding

Contents:

• Installation
  • Stable release (option 1)
  • From sources (option 2)
• Usage
  • In a project
  • Needed files
  • On the command line
  • Via Docker
  • Embedding Evaluation (additional functionality)
• Inputs
• Outputs
  • Logs and Metadata
• Reference
  • cellmaps_coembedding package
• Developer Topics
  • Contributing
  • Development Process
  • Creating a new release
  • Expected configuration for .pypirc file
  • Integration testing
  • Versioning Scheme
• Credits
  • Developers
  • Contributors
• History
  • 1.5.0 (2025-10-23)
  • 1.4.0 (2025-09-10)
  • 1.3.1 (2025-07-03)
  • 1.3.0 (2025-05-29)
  • 1.2.2 (2025-05-15)
  • 1.2.1 (2025-04-14)
  • 1.2.0 (2025-03-19)
  • 1.1.0 (2025-03-05)
  • 1.0.0 (2025-01-28)
  • 0.4.0 (2024-12-02)
  • 0.3.1 (2024-09-13)
  • 0.3.0 (2024-09-06)
  • 0.2.0 (2024-07-17)
  • 0.1.0 (2024-02-12)

Indices and tables

• Index

• Module Index

• Search Page