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 0.2.0

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 0.2.0
File	Size	Uploaded
SummarizedExperiment-0.2.0.tar.gz	26.3 kB	Dec 31, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for summarizedexperiment 0.2.0
File	Interpreter	ABI	Platform	Reset
SummarizedExperiment-0.2.0-py3-none-any.whl 11.2 kB Dec 31, 2022	Python 3	none	any	Details

Total release size: 37.5 kB

Release files / SummarizedExperiment-0.2.0.tar.gz

Download URL	SummarizedExperiment-0.2.0.tar.gz
Size	26.3 kB
Tags	Source
SHA-256 checksum How to use checksums	`3f1275fe38f26b87c95f004a72587a27f0c9f7d8efedd948d3979af15528cdee`
BLAKE2b-256 checksum How to use checksums	`8b02b73e448dab09506e2947d5b072055ca87315e0adb9505b7d703bd8c06f91`
Upload date	Dec 31, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`

Release files / SummarizedExperiment-0.2.0-py3-none-any.whl

Download URL	SummarizedExperiment-0.2.0-py3-none-any.whl
Size	11.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`1866fac767caa731a14baa02cb7b6ee6b2b17183a41c706d31da49f8a7b8a36c`
BLAKE2b-256 checksum How to use checksums	`7789908b3d42a6c67bd670ef4540981cc32257b8b60ed3ea1f6990bc819e14b6`
Upload date	Dec 31, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`