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/.