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 0.2.2

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 0.2.2
File	Size	Uploaded
SummarizedExperiment-0.2.2.tar.gz	26.5 kB	Feb 28, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for summarizedexperiment 0.2.2
File	Interpreter	ABI	Platform	Reset
SummarizedExperiment-0.2.2-py3-none-any.whl 11.4 kB Feb 28, 2023	Python 3	none	any	Details

Total release size: 37.9 kB

Release files / SummarizedExperiment-0.2.2.tar.gz

Download URL	SummarizedExperiment-0.2.2.tar.gz
Size	26.5 kB
Tags	Source
SHA-256 checksum How to use checksums	`46a822fd2142f179fb5acce07be8b70cd3e236e0b2ab79558a8bf20da22a7d2d`
BLAKE2b-256 checksum How to use checksums	`8aa2bef90a7f21c287b22a6d6dc67009a9caaf247c83bbf7a1400a026e9d949a`
Upload date	Feb 28, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`

Release files / SummarizedExperiment-0.2.2-py3-none-any.whl

Download URL	SummarizedExperiment-0.2.2-py3-none-any.whl
Size	11.4 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`64d310f949de5ba85d4e1da1d7b590546e1fe40d97d390cd6fb6a60a3ea8e2c2`
BLAKE2b-256 checksum How to use checksums	`134db9e3b467dad5d7133cd37d69a5461af557d0ae25753c8a5a6d4e77ea4455`
Upload date	Feb 28, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`