Reference

Comprehensive reference documentation for mokume's CLI commands, Python API, configuration options, and output columns.

CLI Reference

All mokume commands and their options in one place.

Python API

Key classes and functions for programmatic usage: quantification methods, normalization, preprocessing filters, data reshaping, FASTA handling, and AnnData creation.

Configuration

PipelineConfig dataclass structure and preprocessing filter YAML format.

Computed Values

Column names and formulas for all output values (iBAQ, TopN, MaxLFQ, TPA, CopyNumber, etc.).