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
Metadata
2 maintainers
Release files for miqc-py 0.0.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| miqc_py-0.0.1.tar.gz | 4.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| miqc_py-0.0.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 7.3 kB
Release files / miqc_py-0.0.1.tar.gz
| Download URL | miqc_py-0.0.1.tar.gz |
|---|---|
| Size | 4.0 kB |
| Tags | Source |
|
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Release files / miqc_py-0.0.1-py3-none-any.whl
| Download URL | miqc_py-0.0.1-py3-none-any.whl |
|---|---|
| Size | 3.3 kB |
| Tags | Python 3 |
|
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