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 0.1.4

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 0.1.4
File	Size	Uploaded
SummarizedExperiment-0.1.4.tar.gz	26.2 kB	Dec 28, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for summarizedexperiment 0.1.4
File	Interpreter	ABI	Platform	Reset
SummarizedExperiment-0.1.4-py3-none-any.whl 10.8 kB Dec 28, 2022	Python 3	none	any	Details

Total release size: 36.9 kB

Release files / SummarizedExperiment-0.1.4.tar.gz

Download URL	SummarizedExperiment-0.1.4.tar.gz
Size	26.2 kB
Tags	Source
SHA-256 checksum How to use checksums	`e2b087d388b8e40844041f784b22e3561d4e59336feeaf01fe03a3b05767f810`
BLAKE2b-256 checksum How to use checksums	`21f79503b1cd2b6b89886ad4e5d49368487fc0bd5930e645c2d3621518d00c2c`
Upload date	Dec 28, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`

Release files / SummarizedExperiment-0.1.4-py3-none-any.whl

Download URL	SummarizedExperiment-0.1.4-py3-none-any.whl
Size	10.8 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`a80a2d5ffdc33ca7c26391bb8011e94081bb50449b2b8069f497415bb8672789`
BLAKE2b-256 checksum How to use checksums	`89b9f38eaccb2a5a82f928a2745b02abdd28c66d1bb4f8c629ef5bcc3f3a777e`
Upload date	Dec 28, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`