Usage

Below are examples on how to use the cellmaps_utils package.

• In a project (RO-Crate)
  • Registering RO-Crate
  • Registering software in RO-Crate
  • Registering dataset in RO-Crate
  • Registering computation in RO-Crate
  • Configuring logging for command line
  • Configuring logging into directory/RO-Crate
• Cell Maps for AI Data Release
  • 1) Perturbation/CRISPR data release (step 1 above)
  • 1) Affinity Purification Mass Spectrometry (AP-MS) data release
• Zmadex/SAINT input format
  • 1) Size Exclusion Chromatography with Mass Spectrometry (SEC-MS) data release
  • 1) Immunofluorescent Image (IFImage) data release
  • 2) Compress RO-Crate from step one
  • 3) Run cellmaps_utilscmd.py rocratetable on RO-Crate files
  • 4) Upload RO-Crate files
  • 5) Send table from Step 4 to admin of CM4AI site
• Hierarchical networks support (CX2/ HCX)
  • HiDeF Converters
  • DDOT Converters
  • CX2 to HCX conversion
  • Uploading interactome and hierarchy to NDEx
  • Hierarchy Robustness