SummarizedExperiment

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

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
)

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

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
File	Size	Uploaded
SummarizedExperiment-0.1.tar.gz	21.1 kB	Jun 15, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for summarizedexperiment 0.1
File	Interpreter	ABI	Platform	Reset
SummarizedExperiment-0.1-py3-none-any.whl 7.0 kB Jun 15, 2022	Python 3	none	any	Details

Total release size: 28.1 kB

Release files / SummarizedExperiment-0.1.tar.gz

Download URL	SummarizedExperiment-0.1.tar.gz
Size	21.1 kB
Tags	Source
SHA-256 checksum How to use checksums	`2e379e64e22c24b7b89cbedd928a70092830e692d2b8ddbde2f37c75cf4ba373`
BLAKE2b-256 checksum How to use checksums	`ef6e081bad79f612712b3c17aa19dbbd3b3466ddf96b5bab899bea280fc5e2da`
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-py3-none-any.whl

Download URL	SummarizedExperiment-0.1-py3-none-any.whl
Size	7.0 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`1f054c7c866ace2756f8a6dc63b1802e4e20b60688c471cea8ada01098a31a25`
BLAKE2b-256 checksum How to use checksums	`a6196590a80c2a5a9181756353504f72fb8f4b606166266759ee1c7379f76f0d`
Upload date	Jun 15, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.13`