Cell Maps Pipeline

The Cell Maps Pipeline takes ImmunoFluorescent images from the Human Protein Atlas along with Affinity Purification Mass Spectrometry data from one or more sources, converts them into embeddings that are then coembedded and converted into an integrated interaction network from which a hierarchical model is derived.

The pipeline invokes seven tools that each create an output directory where results are stored and registered within Research Object Crates (RO-Crate) using the FAIRSCAPE-cli.

Overview of Cell Maps Pipeline

• Free software: MIT license

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

Tools

See links below for more information about the individual tools

• cellmaps_imagedownloader

• cellmaps_ppidownloader

• cellmaps_image_embedding

• cellmaps_ppi_embedding

• cellmaps_coembedding

• cellmaps_generate_hierarchy

• cellmaps_hierarchyeval

Contents:

• Installation
  • Stable release
  • From sources
• Usage
  • Usage via command line
  • Usage programmatically
  • What is and how to create a provenance file
  • Example usage for CM4AI data
  • Example usage using data from Human Protein Atlas and Bioplex
  • Save hierarchy to NDEx
• Outputs
• Reference
  • cellmaps_pipeline package
• Developer Topics
  • Contributing
  • Development Process
  • Creating a new release
  • Expected configuration for .pypirc file
  • Integration testing
  • Versioning Scheme
• Credits
  • Developers
  • Contributors
• History
  • 0.1.0 (2023-05-22)

Indices and tables

• Index

• Module Index

• Search Page