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 0.2.11

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 0.2.11
File	Size	Uploaded
SummarizedExperiment-0.2.11.tar.gz	1.0 MB	Jul 25, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for summarizedexperiment 0.2.11
File	Interpreter	ABI	Platform	Reset
SummarizedExperiment-0.2.11-py3-none-any.whl 21.4 kB Jul 25, 2023	Python 3	none	any	Details

Total release size: 1.0 MB

Release files / SummarizedExperiment-0.2.11.tar.gz

Download URL	SummarizedExperiment-0.2.11.tar.gz
Size	1.0 MB
Tags	Source
SHA-256 checksum How to use checksums	`d9ccfe4988782024b312e3a5277508bd86174e6d87d046875fbefb9026fd1232`
BLAKE2b-256 checksum How to use checksums	`e39bf75b9e57643d4d7a026dbacad30c6e4e95f117398006626551451902ba4d`
Upload date	Jul 25, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.17`

Release files / SummarizedExperiment-0.2.11-py3-none-any.whl

Download URL	SummarizedExperiment-0.2.11-py3-none-any.whl
Size	21.4 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`97848859dff87b988970735b10f3f9fdda7382ad7ae66ffeb10f7a55b34646e9`
BLAKE2b-256 checksum How to use checksums	`d8c789ad697b35e9a3f66adab758e0e937d042ee8406b7174c1befb6eed615ef`
Upload date	Jul 25, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.17`