miqc-py

Python implementation of miQC (paper).

Installation

pip install miqc_py

Usage

Usage follows the scverse API conventions. Parameter names follow the R implementation of miQC.

import miqc_py

# ...

miqc_py.calculate_miqc(adata)
miqc_py.filter_cells(adata)

Plotting

Optionally, we can plot the results with altair (not a dependency of miqc_py - may need to install first).

import altair as alt

alt.Chart(adata.obs).mark_circle().encode(
    x="total_genes_by_counts:Q",
    y="pct_counts_mito:Q",
    color="prob_compromised:Q"
)

Development

conda env create -f environment.yml
conda activate miqc-py

jupyter lab