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
2 maintainers
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