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/.

Metadata

Release files for singlecellexperiment 0.2.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for singlecellexperiment 0.2.1
File	Size	Uploaded
SingleCellExperiment-0.2.1.tar.gz	1.1 MB	Dec 31, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for singlecellexperiment 0.2.1
File	Interpreter	ABI	Platform	Reset
SingleCellExperiment-0.2.1-py3-none-any.whl 8.4 kB Dec 31, 2022	Python 3	none	any	Details

Total release size: 1.1 MB

Release files / SingleCellExperiment-0.2.1.tar.gz

Download URL	SingleCellExperiment-0.2.1.tar.gz
Size	1.1 MB
Tags	Source
SHA-256 checksum How to use checksums	`e3fabac151be21d54def26160cc1d3109bd1e493ea4aaef4d8b42408fa6b2084`
BLAKE2b-256 checksum How to use checksums	`e61621b02cd4340a21322d8f0393955aa35b917e5a3771293b7754897e44d7dd`
Upload date	Dec 31, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`

Release files / SingleCellExperiment-0.2.1-py3-none-any.whl

Download URL	SingleCellExperiment-0.2.1-py3-none-any.whl
Size	8.4 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`1e50ba410de233ba846dbee1a2ed729a8850b1f5b3843d907d072cf5c2336664`
BLAKE2b-256 checksum How to use checksums	`3957e51f288c79b8ceab3e3256bf280bea555114a5f69043fcd3079c61bc0c3a`
Upload date	Dec 31, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`