Installation

From PyPI

pip install mokume

Optional Extras

mokume uses optional dependencies for specialized features:

DirectLFQPlottingBatch CorrectionInteractive ReportsEverything

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 batch correction via the inmoose package.

pip install mokume[reports]

Enables interactive HTML reports with plotly.

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