Installation

From PyPI

pip install mokume

For standard quantification workflows, the core package is enough. Install optional extras only when you need specific functionality.

Optional Extras

mokume uses optional dependencies for specialized features:

DirectLFQPlottingBatch CorrectionInteractive ReportsTissueMapEverything

pip install mokume[directlfq]

Enables DirectLFQ quantification and the DirectLFQ backend for MaxLFQ.

pip install mokume[plotting]

Enables volcano plots, heatmaps, PCA, and box plots (matplotlib + seaborn).

pip install mokume[batch-correction]

Enables ComBat-based batch correction via the combat dependency.

pip install mokume[reports]

Enables interactive HTML reports with plotly.

pip install mokume[tissuemap]

Enables the mokume tissuemap workflow for per-dataset tissue atlas analysis, including AdaTiSS tissue-specificity scoring, embeddings, and atlas plots.

pip install mokume[all]

Installs all optional dependencies.

From Source

git clone https://github.com/bigbio/mokume
cd mokume
pip install .

Using Conda

mamba env create -f environment.yaml
conda activate mokume
pip install .

Requirements

• Python >= 3.9
• Core dependencies: numpy, pandas, scipy, scikit-learn, pyopenms, pyarrow, duckdb, click, anndata