scquill
Approximate any single cell data set, saving >99% of memory and runtime.
It's pronounced /ˈskwɪɹl̩//, like the animal.
Approximating a single cell data set
import scquill
q = scquill.Compressor(
filename='myscdata.h5ad',
output_filename='myapprox.h5',
celltype_column="cell_annotation",
)
q()
Exploring an approximation
To load an approximation:
import scquill
app = scquill.Approximation(
filename='myapprox.h5',
)
To show a dot plot:
scquill.pl.dotplot(app, ['gene1', 'gene2', 'gene3'])
To show a neighborhood plot:
scquill.pl.neighborhoodplot(app, ['gene1', 'gene2', 'gene3'])
To show embeddings of cell neighborhoods, similar to single-cell UMAPs:
scquill.pl.embedding(app, ['gene1', 'gene2', 'gene3'])
MORE TO COME
Authors
Fabio Zanini @fabilab
1 maintainer
Metadata
1 maintainer
Release files for scquill 0.3.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scquill-0.3.2.tar.gz | 19.6 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scquill-0.3.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 45.6 kB
Release files / scquill-0.3.2.tar.gz
| Download URL | scquill-0.3.2.tar.gz |
|---|---|
| Size | 19.6 kB |
| Tags | Source |
|
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poetry/1.8.3 CPython/3.12.6 Linux/6.6.23-1-lts
|
Release files / scquill-0.3.2-py3-none-any.whl
| Download URL | scquill-0.3.2-py3-none-any.whl |
|---|---|
| Size | 26.0 kB |
| Tags | Python 3 |
|
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poetry/1.8.3 CPython/3.12.6 Linux/6.6.23-1-lts
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