Reference

Comprehensive reference documentation for mokume's CLI commands, Python API, configuration options, output columns, TissueMap, differential expression, imputation, and LOESS capabilities.

CLI Reference

All mokume commands and their options in one place, including features2proteins, correct-batches, tissuemap, and tsne-visualization.

Python API

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

Configuration

PipelineConfig and TissueMapConfig dataclass structures, plus preprocessing filter YAML format.

Computed Values

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