SummarizedExperiment

Container to represent genomic experiments, follows Bioconductor's SummarizedExperiment.

Install

Package is published to PyPI

pip install summarizedexperiment

Usage

Currently supports SummarizedExperiment & RangeSummarizedExperiment classes

First create necessary 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,
    }
)

To create a SummarizedExperiment,

from summarizedexperiment import SummarizedExperiment

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

To create a RangeSummarizedExperiment

from summarizedexperiment import RangeSummarizedExperiment

trse = RangeSummarizedExperiment(
    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 0.2.1

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

Source distribution (sdist)

Source distribution for summarizedexperiment 0.2.1
File	Size	Uploaded
SummarizedExperiment-0.2.1.tar.gz	26.3 kB	Jan 24, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for summarizedexperiment 0.2.1
File	Interpreter	ABI	Platform	Reset
SummarizedExperiment-0.2.1-py3-none-any.whl 11.2 kB Jan 24, 2023	Python 3	none	any	Details

Total release size: 37.5 kB

Release files / SummarizedExperiment-0.2.1.tar.gz

Download URL	SummarizedExperiment-0.2.1.tar.gz
Size	26.3 kB
Tags	Source
SHA-256 checksum How to use checksums	`203298c55cc35354ffd04dc430b43de2513279f2e380e14ee736271604537b82`
BLAKE2b-256 checksum How to use checksums	`cf810d5473ba794d789eafc5ff7a1662c6fbff8fef4142634a30c5f5f3db3016`
Upload date	Jan 24, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`

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

Download URL	SummarizedExperiment-0.2.1-py3-none-any.whl
Size	11.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`47f8e7ad8039c51e7b44631f3b94b496d8a59aa33ed9e14568addf43634065c5`
BLAKE2b-256 checksum How to use checksums	`3d368ac8791844f66a377cbd0b44d9bf5cb70575bdfa7158fc9655eae33b5939`
Upload date	Jan 24, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`