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Open Source Science

https://github.com/theislab/ehrdata

A datastructure for EHR data

https://github.com/theislab/ehrdata

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.8%) to scientific vocabulary

Keywords

data-analysis ehr ehrapy
Last synced: 6 months ago · JSON representation

Repository

A datastructure for EHR data

Basic Info
Statistics
  • Stars: 7
  • Watchers: 2
  • Forks: 3
  • Open Issues: 17
  • Releases: 5
Topics
data-analysis ehr ehrapy
Created over 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License

README.md

ehrdata

Tests Documentation

Ehrdata is a data framework that comprises a FAIR storage format and a collection of Python libraries for performant access, alignment, and processing of uni- and multi-modal electronic health record datasets. This repository contains the core ehrdata library. See the ehrapy package for an analysis package that uses ehrdata to enable the analysis of electronic health record datasetes.

Getting started

Please refer to the documentation, in particular, the API documentation.

Disclaimer

ehrdata is under heavy construction, and its API not stable. If you find it potentially interesting for your work, reach out to us via the scverse zulip platform! We can help you using it and will be able to stabilize things you need.

If you have inputs on features, please do not hesitate to open an issue on our issue tracker!

Installation

You need to have Python 3.11 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.

There are several alternative options to install ehrdata:

1) Install the latest release of ehrdata from PyPI:

bash pip install ehrdata

  1. Install the latest development version:

bash pip install git+https://github.com/theislab/ehrdata.git@main

Release notes

See the changelog.

Contact

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Citation

t.b.a

Owner

  • Name: Theis Lab
  • Login: theislab
  • Kind: organization
  • Email: icb.office@helmholtz-muenchen.de
  • Location: Munich

Institute of Computational Biology

GitHub Events

Total
  • Create event: 65
  • Release event: 2
  • Issues event: 55
  • Watch event: 1
  • Delete event: 56
  • Member event: 3
  • Issue comment event: 46
  • Push event: 286
  • Pull request review event: 50
  • Pull request review comment event: 80
  • Pull request event: 116
  • Fork event: 1
Last Year
  • Create event: 65
  • Release event: 2
  • Issues event: 55
  • Watch event: 1
  • Delete event: 56
  • Member event: 3
  • Issue comment event: 46
  • Push event: 286
  • Pull request review event: 50
  • Pull request review comment event: 80
  • Pull request event: 116
  • Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 43
  • Total pull requests: 94
  • Average time to close issues: 2 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 5
  • Total pull request authors: 10
  • Average comments per issue: 0.26
  • Average comments per pull request: 0.39
  • Merged pull requests: 67
  • Bot issues: 0
  • Bot pull requests: 36
Past Year
  • Issues: 41
  • Pull requests: 80
  • Average time to close issues: 2 months
  • Average time to close pull requests: 6 days
  • Issue authors: 4
  • Pull request authors: 9
  • Average comments per issue: 0.27
  • Average comments per pull request: 0.35
  • Merged pull requests: 56
  • Bot issues: 0
  • Bot pull requests: 26
View more stats
Top Authors
Issue Authors
  • eroell (26)
  • Zethson (10)
  • MDLDan (4)
  • xinyuejohn (2)
  • flying-sheep (1)
Pull Request Authors
  • pre-commit-ci[bot] (36)
  • eroell (32)
  • Zethson (13)
  • flying-sheep (4)
  • scverse-bot (3)
  • ShreyParikh07 (2)
  • aGuyLearning (1)
  • MDLDan (1)
  • xinyuejohn (1)
  • agerardy (1)
Top Labels
Issue Labels
enhancement (38) bug (4)
Pull Request Labels
enhancement (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 515 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 8
  • Total maintainers: 2
pypi.org: ehrdata

A Python package for EHR data

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 515 Last month
Rankings
Dependent packages count: 10.2%
Average: 34.0%
Dependent repos count: 57.7%
Maintainers (2)
zethson eroell
Last synced: 6 months ago

Dependencies

.github/workflows/build.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/release.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/test.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • codecov/codecov-action v3 composite
pyproject.toml pypi
  • anndata *
  • session-info *