SummarizedExperiment

Container to represent data from genomic experiments, follows Bioconductor's SummarizedExperiment. It uses efficient structures already available in the Pandas/numpy eco-system & adds a familiar interface.

Install

Package is published to PyPI

pip install summarizedexperiment

Usage

Currently supports both SummarizedExperiment & RangeSummarizedExperiment objects

First create necessary sample data

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,

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

To create a RangeSummarizedExperiment

trse = SummarizedExperiment(
    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 0.1.2

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 0.1.2
File	Size	Uploaded
SummarizedExperiment-0.1.2.tar.gz	22.0 kB	Jun 15, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for summarizedexperiment 0.1.2
File	Interpreter	ABI	Platform	Reset
SummarizedExperiment-0.1.2-py3-none-any.whl 7.6 kB Jun 15, 2022	Python 3	none	any	Details

Total release size: 29.6 kB

Release files / SummarizedExperiment-0.1.2.tar.gz

Download URL	SummarizedExperiment-0.1.2.tar.gz
Size	22.0 kB
Tags	Source
SHA-256 checksum How to use checksums	`665f80ff4a5ca27f21b598f61bfcf2af7c9126e2ae8bbd6960cd78cc0bd37a64`
BLAKE2b-256 checksum How to use checksums	`826e4f2f6f9388c4362b78f860106b46c51b9ec92c556b9b893a1567eb7119bc`
Upload date	Jun 15, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.13`

Release files / SummarizedExperiment-0.1.2-py3-none-any.whl

Download URL	SummarizedExperiment-0.1.2-py3-none-any.whl
Size	7.6 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`7a54fbaf2678592bfb3efbe3c138fd4e7c58d82130b419297b4f8b9064ba6648`
BLAKE2b-256 checksum How to use checksums	`930df63ec4bdb02adb98cdcf0858c1f781cb870b7226137f6a85c99f44adc038`
Upload date	Jun 15, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.13`