SingleCellExperiment

Container class for representing data from single-cell experiments; follows Bioconductor's SingleCellExperiment.

Install

Package is published to PyPI

pip install singlecellexperiment

Usage

First create mock sample data

import pandas as pd
import numpy as np
from genomicranges import GenomicRanges

nrows = 200
ncols = 6
counts = np.random.rand(nrows, ncols)
df_gr = pd.DataFrame(
    {
        "seqnames": [
            "chr1",
            "chr2",
            "chr2",
            "chr2",
            "chr1",
            "chr1",
            "chr3",
            "chr3",
            "chr3",
            "chr3",
        ]
        * 20,
        "starts": range(100, 300),
        "ends": range(110, 310),
        "strand": ["-", "+", "+", "*", "*", "+", "+", "+", "-", "-"] * 20,
        "score": range(0, 200),
        "GC": [random() for _ in range(10)] * 20,
    }
)

gr = GenomicRanges.fromPandas(df_gr)

colData = pd.DataFrame(
    {
        "treatment": ["ChIP", "Input"] * 3,
    }
)

from singlecellexperiment import SingleCellExperiment

tse = SingleCellExperiment(
    assays={"counts": counts}, rowData=df_gr, colData=colData
)

For more use cases including subset, 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 0.1

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 0.1
File	Size	Uploaded
SingleCellExperiment-0.1.tar.gz	22.5 kB	Jun 16, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for singlecellexperiment 0.1
File	Interpreter	ABI	Platform	Reset
SingleCellExperiment-0.1-py3-none-any.whl 7.0 kB Jun 16, 2022	Python 3	none	any	Details

Total release size: 29.5 kB

Release files / SingleCellExperiment-0.1.tar.gz

Download URL	SingleCellExperiment-0.1.tar.gz
Size	22.5 kB
Tags	Source
SHA-256 checksum How to use checksums	`39cc66c46dd159cbdb078e5e5467c5859be829dacff6532943e5b8ec090f3798`
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Upload date	Jun 16, 2022
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Uploaded via	`twine/4.0.1 CPython/3.9.13`

Release files / SingleCellExperiment-0.1-py3-none-any.whl

Download URL	SingleCellExperiment-0.1-py3-none-any.whl
Size	7.0 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`214307c3e3d9a9f40fc6024a101649850b039c292faa41866cf2982a7a5f582c`
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Upload date	Jun 16, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.13`