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https://github.com/broadinstitute/genomeshader

Visualization of biobank-scale genomic datasets.

https://github.com/broadinstitute/genomeshader

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.2%) to scientific vocabulary

Keywords from Contributors

projection interactive generic sequences archival pipelines genomics observability autograding hacking
Last synced: 10 months ago · JSON representation

Repository

Visualization of biobank-scale genomic datasets.

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: bsd-3-clause
  • Language: HTML
  • Default Branch: main
  • Homepage:
  • Size: 5.64 MB
Statistics
  • Stars: 3
  • Watchers: 5
  • Forks: 0
  • Open Issues: 9
  • Releases: 0
Created over 2 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.rst 

genomeshader
""""""""""""

|GitHub release| |PyPI version genomeshader|

.. |GitHub release| image:: https://img.shields.io/github/release/broadinstitute/genomeshader.svg
   :target: https://github.com/broadinstitute/genomeshader/releases/

.. |PyPI version genomeshader| image:: https://img.shields.io/pypi/v/genomeshader.svg
   :target: https://pypi.python.org/pypi/genomeshader/

Genomeshader is a Rust-backed Python library for rapid visualization of read-level data spanning variants across huge numbers of samples. It is intended for use within Jupyter notebooks.

Documentation for the API can be found on the `documentation page `_.


Prerequisites
-------------

Genomeshader is designed to access local files or data in Google Cloud Storage (GCS). Within certain cloud-computing environments (i.e. Terra, All of Us Researcher Workbench), access to GCS is already configured. For accessing files in GCS on your local machine, you will also need to install the `Google Cloud CLI `_. Then, configure your `Application Default Credentials (ADC) `_.


Installation
------------

``pip`` is recommended for installation.

::

   pip install genomeshader 



Building from source
--------------------

To build from source (particularly for those interested in contributing to the code), follow the procedure below.

.. code-block:: bash

   # Clone repository.
   git clone https://github.com/broadinstitute/genomeshader.git
   cd genomeshader

   # Create a Python virtual environment and install Maturin, the tool that
   # will compile the Rust and Python code into a complete library.
   # For more information on Maturin, visit https://github.com/PyO3/maturin .
   python -mvenv venv
   . venv/bin/activate
   pip install maturin

   # Build the library (with release optimizations) and install it in
   # the currently active virtual environment.
   maturin develop --release

Supported platforms
-------------------

Genomeshader is compiled for Linux and MacOSX. Windows is not currently supported.

Getting help
------------

If you encounter bugs or have questions/comments/concerns, please file an issue on our `Github page `_.

Developers' guide
-----------------

For information on contributing to Genomeshader development, visit our `developer documentation `_.

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

Total
Last Year

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 212
  • Total Committers: 3
  • Avg Commits per committer: 70.667
  • Development Distribution Score (DDS): 0.363
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Kiran V Garimella k****n@b****g 135
BumpVersion Action b****n@g****s 75
dependabot[bot] 4****] 2
Committer Domains (Top 20 + Academic)
broadinstitute.org: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 8
  • Total pull requests: 5
  • Average time to close issues: 8 days
  • Average time to close pull requests: 7 days
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 0.13
  • Average comments per pull request: 0.2
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 5
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • bshifaw (4)
  • kvg (3)
  • ArunGaonkar (1)
Pull Request Authors
  • dependabot[bot] (10)
Top Labels
Issue Labels
good first issue (3) enhancement (2) bug (1)
Pull Request Labels
dependencies (10) rust (5) python (5)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 282 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 73
  • Total maintainers: 1
pypi.org: genomeshader

Fast visualization of genomic data

  • Versions: 73
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 282 Last month
Rankings
Dependent packages count: 10.0%
Average: 38.1%
Dependent repos count: 66.2%
Maintainers (1)
kgarimella
Last synced: 11 months ago

Dependencies

.github/workflows/release.yml actions
  • PyO3/maturin-action v1 composite
  • WyriHaximus/github-action-get-previous-tag v1 composite
  • actions/checkout master composite
  • actions/checkout v2 composite
  • actions/checkout v3 composite
  • actions/create-release v1 composite
  • actions/download-artifact v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • ad-m/github-push-action master composite
  • christian-draeger/read-properties 1.0.0 composite
  • jasonamyers/github-bumpversion-action v1.0.4 composite
  • rtCamp/action-slack-notify v2.0.2 composite
Cargo.lock cargo
  • 607 dependencies
Cargo.toml cargo
pyproject.toml pypi
  • datashader *
  • holoviews *
  • polars *
requirements.txt pypi
  • appnope ==0.1.3
  • backcall ==0.2.0
  • debugpy ==1.7.0
  • decorator ==5.1.1
  • entrypoints ==0.4
  • ipykernel ==6.16.2
  • ipython ==8.10.0
  • jedi ==0.19.1
  • jupyter-client ==7.4.9
  • jupyter-core ==4.12.0
  • matplotlib-inline ==0.1.6
  • maturin ==1.4.0
  • nest-asyncio ==1.5.8
  • packaging ==23.2
  • parso ==0.8.3
  • pexpect ==4.9.0
  • pickleshare ==0.7.5
  • prompt-toolkit ==3.0.43
  • psutil ==5.9.7
  • ptyprocess ==0.7.0
  • pygments ==2.17.2
  • python-dateutil ==2.8.2
  • pyzmq ==25.1.2
  • six ==1.16.0
  • tomli ==2.0.1
  • tornado ==6.3.3
  • traitlets ==5.9.0
  • wcwidth ==0.2.12
dev-requirements.txt pypi
  • datashader ==0.15.2 development
  • holoviews ==1.17.1 development
  • ipykernel ==6.28.0 development
  • maturin ==1.4.0 development
  • panel ==1.2.3 development
  • polars ==0.20.4 development
  • pyparsing ==3.1.1 development