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BiocPy

Facilitate Bioconductor Workflows in Python
README.md

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BiocPy: Facilitate Bioconductor Workflows in Python

BiocPy brings Bioconductor's core data structures and analysis tools to the Python ecosystem. These structures, including BiocFrame and GenomicRanges, serve as essential and foundational data structures, acting as the building blocks for extensive and complex representations. For example, container classes like SummarizedExperiment, SingleCellExperiment, and MultiAssayExperiment represent single or multi-omic experimental data and metadata.

Note

Resources:

Core Packages

For a complete list of packages, visit our GitHub organization.

Data Structures

Package Description PyPI Links
BiocFrame Bioconductor-like data frames PyPI GitHub | Docs
IRanges Interval arithmetic operations PyPI GitHub | Docs | Bioconductor
GenomicRanges Genomic location analysis PyPI GitHub | Docs | Bioconductor

Containers

Package Description PyPI Links
SummarizedExperiment Genomic experiments container PyPI GitHub | Docs | Bioconductor
SingleCellExperiment Single-cell genomics container PyPI GitHub | Docs | Bioconductor
MultiAssayExperiment Multi-omics data framework PyPI GitHub | Docs | Bioconductor

R Interoperability

Package Description PyPI Links
rds2py Read RDS files directly in Python PyPI GitHub | Docs
BiocUtils Common utilities mirroring R's base functionality PyPI GitHub | Docs
mopsy Matrix operations with R-like syntax PyPI GitHub | Docs
pyBiocFileCache Resource caching system PyPI GitHub | Docs

Friends of BiocPy

BiocPy integrates with several analysis tools and frameworks

Analysis Tools

  • libscran: Multi-model single-cell analysis in R, Python and JavaScript.
  • SingleR-inc: Cell type annotation for single-cell data.

Data Management

  • ArtifactDB: Language-agnostic access to data across computational environments.
  • tatami-inc: Read various matrix representations through a common interface.

Model Training

  • TileOme: TileDB-based genomic data storage with AI/ML dataloaders.

Installation

All packages in the BiocPy are published to PyPI. Install the core packages using the biocpy wrapper:

pip install biocpy

Individual packages can be installed separately. See each package's documentation for specific installation instructions.

Contributing

We welcome contributions! Check out our developer guide to get started.

Pinned Loading

  1. rds2py rds2py Public

    Read RDS files, in Python

    Python 19 3

  2. GenomicRanges GenomicRanges Public

    Container class to represent genomic locations and support genomic analysis

    Python 17 4

  3. SummarizedExperiment SummarizedExperiment Public

    Container class for genomic experiments

    Python 5 2

  4. SingleCellExperiment SingleCellExperiment Public

    Container class for single-cell experiments

    Python 6 1

  5. scrnaseq scrnaseq Public

    Collection of public single-cell RNA-seq datasets

    Python 1

Repositories

Showing 10 of 27 repositories
  • SpatialExperiment Public

    Container for Spatial Experiments

    BiocPy/SpatialExperiment’s past year of commit activity
    Python 0 MIT 0 0 1 Updated Jan 22, 2025
  • SingleCellExperiment Public

    Container class for single-cell experiments

    BiocPy/SingleCellExperiment’s past year of commit activity
    Python 6 MIT 1 0 1 Updated Jan 21, 2025
  • .github Public
    BiocPy/.github’s past year of commit activity
    0 0 0 0 Updated Jan 21, 2025
  • pyBiocFileCache Public

    Python implementation of the BiocFileCache R package

    BiocPy/pyBiocFileCache’s past year of commit activity
    Python 1 MIT 2 1 1 Updated Jan 20, 2025
  • SummarizedExperiment Public

    Container class for genomic experiments

    BiocPy/SummarizedExperiment’s past year of commit activity
    Python 5 MIT 2 3 1 Updated Jan 20, 2025
  • GenomicRanges Public

    Container class to represent genomic locations and support genomic analysis

    BiocPy/GenomicRanges’s past year of commit activity
    Python 17 MIT 4 5 (4 issues need help) 1 Updated Jan 20, 2025
  • BiocFrame Public

    Bioconductor-like data frames

    BiocPy/BiocFrame’s past year of commit activity
    Python 4 MIT 3 0 1 Updated Jan 20, 2025
  • scrnaseq Public

    Collection of public single-cell RNA-seq datasets

    BiocPy/scrnaseq’s past year of commit activity
    Python 1 MIT 0 0 1 Updated Jan 20, 2025
  • rds2py Public

    Read RDS files, in Python

    BiocPy/rds2py’s past year of commit activity
    Python 19 MIT 3 0 1 Updated Jan 20, 2025
  • mopsy Public

    Matrix operations

    BiocPy/mopsy’s past year of commit activity
    Python 0 MIT 1 1 1 Updated Jan 20, 2025
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