SingleCellExperiment
Container class to represent single-cell experiments; follows Bioconductor's SingleCellExperiment.
Install
Package is published to PyPI
pip install singlecellexperiment
Usage
Readers are available to read AnnData, H5AD or 10x (MTX, H5) V3 formats as SingleCellExperiment objects.
import singlecellexperiment
sce = singlecellexperiment.read_h5ad("tests/data/adata.h5ad")
## output
class: SingleCellExperiment
dimensions: (20, 30)
assays(3): ['array', 'sparse', 'X']
row_data columns(5): ['var_cat', 'cat_ordered', 'int64', 'float64', 'uint8']
row_names(0):
column_data columns(5): ['obs_cat', 'cat_ordered', 'int64', 'float64', 'uint8']
column_names(0):
main_experiment_name:
reduced_dims(0): []
alternative_experiments(0): []
row_pairs(0): []
column_pairs(0): []
metadata(2): O_recarray nested
OR construct one from scratch
from singlecellexperiment import SingleCellExperiment
tse = SingleCellExperiment(
assays={"counts": counts}, row_data=df_gr, col_data=col_data,
reduced_dims={"tsne": ..., "umap": ...}, alternative_experiments={"atac": ...}
)
Since SingleCellExperiment extends SummarizedExperiment, most methods especially slicing and accessors are applicable here. Checkout the documentation for more info.
Note
This project has been set up using PyScaffold 4.5. For details and usage information on PyScaffold see https://pyscaffold.org/.
Release files for singlecellexperiment 0.4.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| SingleCellExperiment-0.4.1.tar.gz | 1.1 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| SingleCellExperiment-0.4.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.1 MB
Release files / SingleCellExperiment-0.4.1.tar.gz
| Download URL | SingleCellExperiment-0.4.1.tar.gz |
|---|---|
| Size | 1.1 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
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Release files / SingleCellExperiment-0.4.1-py3-none-any.whl
| Download URL | SingleCellExperiment-0.4.1-py3-none-any.whl |
|---|---|
| Size | 14.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/4.0.2 CPython/3.9.18
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