SummarizedExperiment

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

Install

Package is published to PyPI

pip install summarizedexperiment

Usage

Currently supports SummarizedExperiment & RangedSummarizedExperiment 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.from_pandas(df_gr)

colData = pd.DataFrame(
    {
        "treatment": ["ChIP", "Input"] * 3,
    }
)

To create a SummarizedExperiment,

from summarizedexperiment import SummarizedExperiment

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

To create a RangedSummarizedExperiment

from summarizedexperiment import RangedSummarizedExperiment

trse = RangedSummarizedExperiment(
    assays={"counts": counts}, row_ranges=gr, col_data=colData
)

For more use cases including subset, checkout the documentation

Note

This project has been set up using PyScaffold 4.5. For details and usage information on PyScaffold see https://pyscaffold.org/.

Release files for summarizedexperiment 0.3.0

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 0.3.0
File	Size	Uploaded
SummarizedExperiment-0.3.0.tar.gz	1.0 MB	Aug 21, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for summarizedexperiment 0.3.0
File	Interpreter	ABI	Platform	Reset
SummarizedExperiment-0.3.0-py3-none-any.whl 23.1 kB Aug 21, 2023	Python 3	none	any	Details

Total release size: 1.0 MB

Release files / SummarizedExperiment-0.3.0.tar.gz

Download URL	SummarizedExperiment-0.3.0.tar.gz
Size	1.0 MB
Tags	Source
SHA-256 checksum How to use checksums	`b5f6238b1399e6f13affa31de683e136e9fefeed3c1f4a1d41d00e833acc7302`
BLAKE2b-256 checksum How to use checksums	`bfb8e8bd18365325d549bcf0c837eec5ad32eafa85c6492c7e4d81c233db797a`
Upload date	Aug 21, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.17`

Release files / SummarizedExperiment-0.3.0-py3-none-any.whl

Download URL	SummarizedExperiment-0.3.0-py3-none-any.whl
Size	23.1 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`6468a8ee10db1e61d6c3c348e6ac9900d35f062820634916c29ae27e6af32751`
BLAKE2b-256 checksum How to use checksums	`bdaba83583bb995a228c10e8ec911382931097e94fcbd2d2a3e4420510ebdc0f`
Upload date	Aug 21, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.17`