SingleCellExperiment 0.2.2

Container class for single-cell experiments

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.readH5AD("tests/data/adata.h5ad")

OR construct one from scratch

from singlecellexperiment import SingleCellExperiment

tse = SingleCellExperiment(
    assays={"counts": counts}, rowData=df_gr, colData=colData,
    reducedDims={"tsne": ..., "umap": ...}, altExps={"atac": ...}
)

SingleCellExperiment extends SummarizedExperiment, so most methods from there are applicable here. checkout the documentation.

Note

This project has been set up using PyScaffold 4.1.1. For details and usage information on PyScaffold see https://pyscaffold.org/.