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Open Source Science

https://github.com/databio/geniml

Genomic interval machine learning

https://github.com/databio/geniml

Science Score: 26.0%

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
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    DOI references
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    Academic publication links
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    Academic email domains
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.8%) to scientific vocabulary

Keywords

genomic-intervals machine-learning representation-learning
Last synced: 5 months ago · JSON representation

Repository

Genomic interval machine learning

Basic Info
Statistics
  • Stars: 20
  • Watchers: 8
  • Forks: 3
  • Open Issues: 7
  • Releases: 15
Topics
genomic-intervals machine-learning representation-learning
Created over 2 years ago · Last pushed 6 months ago
Metadata Files
Readme License

README.md

Genomic interval machine learning (geniml)

Geniml is a python package for building machine learning models of genomic interval data (BED files). It also includes ancillary functions to support other types of analyses of genomic interval data.

Documentation is hosted at https://docs.bedbase.org/geniml/.

Installation

To install geniml use this commands.

Without specifying dependencies, the default dependencies will be installed, which DO NOT include machine learning (ML) or heavy processing libraries.

From pypi: pip install geniml or install the latest version from the GitHub repository: pip install git+https://github.com/databio/geniml.git

To install Machine learning dependencies use this command:

From pypi: pip install geniml[ml]

Development

Run tests (from /tests) with pytest. Please read the contributor guide to contribute.

Owner

  • Name: Databio
  • Login: databio
  • Kind: organization
  • Location: University of Virginia

Solving problems in computational biology

GitHub Events

Total
  • Create event: 7
  • Issues event: 2
  • Release event: 6
  • Watch event: 4
  • Issue comment event: 8
  • Push event: 8
  • Pull request event: 3
  • Fork event: 2
Last Year
  • Create event: 7
  • Issues event: 2
  • Release event: 6
  • Watch event: 4
  • Issue comment event: 8
  • Push event: 8
  • Pull request event: 3
  • Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 3
  • Average time to close issues: 3 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 7
  • Total pull request authors: 2
  • Average comments per issue: 0.63
  • Average comments per pull request: 0.33
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 days
  • Issue authors: 3
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.33
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • donaldcampbelljr (2)
  • FGQ-FGQ (1)
  • jkanche (1)
  • nleroy917 (1)
  • saanikat (1)
  • jwokaty (1)
  • LimKaiShi (1)
Pull Request Authors
  • jwokaty (2)
  • nleroy917 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 244 last-month
  • Total dependent packages: 3
  • Total dependent repositories: 0
  • Total versions: 14
  • Total maintainers: 2
pypi.org: geniml

Genomic interval toolkit

  • Versions: 14
  • Dependent Packages: 3
  • Dependent Repositories: 0
  • Downloads: 244 Last month
Rankings
Dependent packages count: 10.1%
Average: 38.5%
Dependent repos count: 66.9%
Maintainers (2)
nsheff databio
Last synced: 6 months ago

Dependencies

.github/workflows/black.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • psf/black stable composite
.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
pyproject.toml pypi
requirements/requirements-test.txt pypi
  • pytest * test
  • pytest-remotedata * test
requirements/requirements-train.txt pypi
  • hnswlib *
  • numba *
setup.py pypi
.github/workflows/run-pytest-dev.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v5 composite
.github/workflows/run-pytest-release.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
requirements/requirements-basic.txt pypi
  • boto3 >=1.34.54
  • botocore >=1.34.54
  • genomicranges >=0.4.1
  • gtars >=0.0.15
  • iranges >=0.2.11
  • logmuse >=0.2.8
  • numpy >=1.24.0
  • peppy >=0.40.6
  • pyarrow >=17.0.0
  • pybiocfilecache >=0.4.0
  • pyyaml >=6.0.1
  • requests >=2.31.0
  • s3fs >=2024.3.1
  • ubiquerg >=0.6.3
  • zarr >=2.17.2
requirements/requirements-ml.txt pypi
  • anndata >0.9.0
  • fastembed >=0.2.5
  • gensim >=4.3.3
  • hmmlearn >=0.3.2
  • hnswlib >=0.8.0
  • huggingface_hub >=0.25.1
  • langchain-huggingface ==0.0.2
  • lightning >=2.4.0
  • paramiko >=3.0.0
  • pyBigWig >=0.3.23
  • qdrant_client >=1.11.2
  • scanpy >=1.10.3
  • scipy >=1.13.1
  • torch >=2.3.0