SummarizedExperiment

Container to represent data from genomic experiments, follows Bioconductor's SummarizedExperiment. It uses efficient structures already available in the Pandas/numpy eco-system & adds a familiar interface.

Install

Package is deployed to PyPI

pip install summarizedexperiment

Usage

Currently supports both SummarizedExperiment & RangeSummarizedExperiment objects

First create necessary sample data

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,
    }
)

To create a SummarizedExperiment,

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

To create a RangeSummarizedExperiment

trse = SummarizedExperiment(
    assays={"counts": counts}, rowRanges=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/.

Release files for summarizedexperiment 0.1.1

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

Source distribution (sdist)

Source distribution for summarizedexperiment 0.1.1
File	Size	Uploaded
SummarizedExperiment-0.1.1.tar.gz	21.8 kB	Jun 15, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for summarizedexperiment 0.1.1
File	Interpreter	ABI	Platform	Reset
SummarizedExperiment-0.1.1-py3-none-any.whl 7.3 kB Jun 15, 2022	Python 3	none	any	Details

Total release size: 29.2 kB

Release files / SummarizedExperiment-0.1.1.tar.gz

Download URL	SummarizedExperiment-0.1.1.tar.gz
Size	21.8 kB
Tags	Source
SHA-256 checksum How to use checksums	`340dca5b3a5dbc067ce282550de5e8306ae6ebd57024b136f13d8e12fbd0c843`
BLAKE2b-256 checksum How to use checksums	`72c6f86011504cd48a88566ce375a9fdadea2e026511c551fcb6550f9f4bb499`
Upload date	Jun 15, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.13`

Release files / SummarizedExperiment-0.1.1-py3-none-any.whl

Download URL	SummarizedExperiment-0.1.1-py3-none-any.whl
Size	7.3 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`2656c694856206763941ef1d5b27e3507e3ffd1f11c4e41dab0022cadb06cf39`
BLAKE2b-256 checksum How to use checksums	`3591b90860298e56dd9de40a3947ae59a9531a6d01cee7399c284f927877ae95`
Upload date	Jun 15, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.13`