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biopeaks

biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals - Published in JOSS (2020)

https://github.com/jancbrammer/biopeaks

Science Score: 98.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

biosignals bitalino breathing breathing-rate ecg edf electrophysiology gui heart heart-rate opensignals peak-detection ppg python signal-analysis

Keywords from Contributors

mesh

Scientific Fields

Mathematics Computer Science - 84% confidence
Last synced: 4 months ago · JSON representation ·

Repository

A graphical user interface for feature extraction from heart- and breathing biosignals.

Basic Info
Statistics
  • Stars: 70
  • Watchers: 3
  • Forks: 6
  • Open Issues: 7
  • Releases: 12
Topics
biosignals bitalino breathing breathing-rate ecg edf electrophysiology gui heart heart-rate opensignals peak-detection ppg python signal-analysis
Created almost 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Code of conduct Citation Zenodo

README.md

logo

CI codecov DOI PyPI version JOSS

General Information

biopeaks is a straightforward graphical user interface for feature extraction from electrocardiogram (ECG), photoplethysmogram (PPG) and breathing biosignals. It processes these biosignals semi-automatically with sensible defaults and offers the following functionality:

  • processes files in the open biosignal formats EDF, OpenSignals (Bitalino) as well as plain text files (.txt, .csv, .tsv)
  • interactive biosignal visualization
  • biosignal segmentation
  • benchmarked, automatic extrema detection (R-peaks in ECG, systolic peaks in PPG, exhalation troughs and inhalation peaks in breathing signals) with signal-specific, sensible defaults
  • automatic state-of-the-art artifact correction for ECG and PPG extrema
  • manual editing of extrema
  • extraction of instantaneous features: (heart- or breathing-) rate and period, as well as breathing amplitude
  • .csv export of extrema and instantaneous features for further analysis (e.g., heart rate variability)
  • automatic analysis of multiple files (batch processing)

GUI

Installation

biopeaks can be installed from PyPI:

pip install biopeaks

You can find more details on the installation here.

Documentation

Have a look at the user guide to get started with biopeaks.

Contributors welcome

Improvements or additions to the repository (documentation, tests, code) are welcome and encouraged. Spotted a typo in the documentation? Caught a bug in the code? Ideas for improving the documentation, increase test coverage, or adding features to the GUI? Get started with the contributor guide.

Citation

Please refer to the biopeaks paper in The Journal of Open Source Software.

Changelog

Have a look at the changelog to get an overview of what has changed throughout the versions of biopeaks.

Owner

  • Name: Jan C. Brammer
  • Login: JanCBrammer
  • Kind: user

JOSS Publication

biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals
Published
October 27, 2020
DOI
Volume 5, Issue 54, Page 2621
Authors
Jan C. Brammer ORCID
Behavioral Science Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
Editor
Olivia Guest ORCID
Tags
GUI biosignals heart breathing PPG ECG feature extraction
View PDF Review Thread Software Archive

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "You can cite this software as below."
authors:
- family-names: "Brammer"
  given-names: "Jan C."
  orcid: "https://orcid.org/0000-0002-7664-3753"
title: "biopeaks"
version: 1.4.4
doi: 10.5281/zenodo.3698561
date-released: 2022-01-04
url: "https://github.com/JanCBrammer/biopeaks"
preferred-citation:
  type: article
  authors:
  - family-names: "Brammer"
    given-names: "Jan C."
    orcid: "https://orcid.org/0000-0002-7664-3753"
  doi: "10.21105/joss.02621"
  journal: "Journal of Open Source Software"
  title: "biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals"
  volume: 5
  year: 2020

GitHub Events

Total
  • Issues event: 1
  • Watch event: 5
Last Year
  • Issues event: 1
  • Watch event: 5

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 497
  • Total Committers: 3
  • Avg Commits per committer: 165.667
  • Development Distribution Score (DDS): 0.012
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jan C. Brammer j****r@g****m 491
Stefan Appelhoff s****f@m****g 5
dependabot[bot] 4****] 1
Committer Domains (Top 20 + Academic)
mailbox.org: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 23
  • Total pull requests: 5
  • Average time to close issues: 5 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 5
  • Total pull request authors: 3
  • Average comments per issue: 1.57
  • Average comments per pull request: 0.4
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • sappelhoff (10)
  • JanCBrammer (6)
  • TomDonoghue (5)
  • DominiqueMakowski (1)
  • skywalkerzhang (1)
Pull Request Authors
  • JanCBrammer (2)
  • sappelhoff (2)
  • dependabot[bot] (1)
Top Labels
Issue Labels
JOSS review (15) high priority (4) help wanted (1) feature (1)
Pull Request Labels
JOSS review (2) dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 154 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 19
  • Total maintainers: 1
pypi.org: biopeaks

A graphical user interface for feature extraction from heart- and breathing biosignals.

  • Versions: 19
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 154 Last month
Rankings
Stargazers count: 9.1%
Dependent packages count: 10.1%
Forks count: 14.2%
Average: 14.4%
Downloads: 16.8%
Dependent repos count: 21.5%
Maintainers (1)
jancbrammer
Last synced: 4 months ago

Dependencies

pyproject.toml pypi
  • aiohttp >=3.8.1 develop
  • flake8 >=4.0.1 develop
  • h5py >=3.6.0 develop
  • pytest >=6.2.5 develop
  • pytest-cov >=3.0.0 develop
  • pytest-qt >=4.0.2 develop
  • wfdb >=3.4.1 develop
  • PySide6 >=6.2.2
  • matplotlib >=3.5.0
  • numpy >=1.22.0
  • pandas >=1.3.5
  • pyinstaller >=4.7
  • python >=3.9,<3.11
  • scipy >=1.7.3
.github/workflows/CI.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • codecov/codecov-action v4 composite
  • snok/install-poetry v1 composite