Welcome to illico’s documentation

Contents:

• Overview
• Installation
• How to use
  • DE genes compared to control cells
  • DE genes for clustering analyses
  • Integrating with Scanpy
  • Subsetting the groups to test
  • Excluding some cells in the OVO scenario
  • Excluding some cells from the “rest” in the OVR scenario
• Results and expectations
  • illico is not faster than scanpy or pdex, is there a bug?
  • illico’s results (p-values or fold-change) do not match pdex or scanpy.
• Normalization and log1p
• What if my adata does not fit in memory?
  • Note on Dask support
• How it works
• Benchmarks
  • Benchmarking against other solutions
  • Scalability
• Contributing
  • Testing
• API Reference

Indices and tables

• Index

• Module Index

• Search Page