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ecotyper-py
ecotyper-py

Getting started

  • Installation
  • Quickstart
  • Concepts

Tutorials

  • Tutorials
    • Tutorial 1: Recovery of cell states and ecotypes in bulk data
    • Tutorial 2: Recovery of cell states and ecotypes in scRNA-seq data
    • Tutorial 3: Recovery of cell states and ecotypes in Visium spatial data
    • Tutorial 4: De novo discovery of cell states and ecotypes in bulk data
    • Tutorial 5: De novo discovery of cell states and ecotypes in scRNA-seq data
    • Tutorial 6: De novo discovery from presorted cell populations

Reference

  • Command line
  • API reference
    • ecotyper.api
    • ecotyper.workflows
    • ecotyper.io
    • ecotyper.builtin
    • ecotyper.model
    • ecotyper.recovery_steps
    • ecotyper.discovery_steps
    • ecotyper.discovery_scrna
    • ecotyper.nmf
    • ecotyper.rlayout
    • ecotyper.validate
    • ecotyper.cli
    • ecotyper.rcompat
      • ecotyper.rcompat.cluster
      • ecotyper.rcompat.collate
      • ecotyper.rcompat.fma
      • ecotyper.rcompat.frame
      • ecotyper.rcompat.io
      • ecotyper.rcompat.parse
      • ecotyper.rcompat.rng
      • ecotyper.rcompat.stats
  • Benchmarks: Python vs R
  • Performance: exact mode, fast mode and the alternative solver
  • Validation against R
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