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divbrowse

A web application for interactive visualization and exploratory data analysis of variant call matrices

https://github.com/ipk-bit/divbrowse

Science Score: 57.0%

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  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (15.0%) to scientific vocabulary

Keywords

bioinformatics data-visualization genomics genomics-analysis genomics-data genomics-visualization gff3 principal-component-analysis vcf visualization
Last synced: 4 months ago · JSON representation ·

Repository

A web application for interactive visualization and exploratory data analysis of variant call matrices

Basic Info
Statistics
  • Stars: 20
  • Watchers: 2
  • Forks: 3
  • Open Issues: 5
  • Releases: 2
Topics
bioinformatics data-visualization genomics genomics-analysis genomics-data genomics-visualization gff3 principal-component-analysis vcf visualization
Created over 4 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.md


PyPI Docker Image Version (latest semver) GitHub release (latest SemVer)

Peer-reviewed paper in GigaScience Journal

Documentation Status Python PyPI Downloads Libraries.io dependency status for latest release License


Website: https://divbrowse.ipk-gatersleben.de
Documentation: https://divbrowse.readthedocs.io
Paper: https://doi.org/10.1093/gigascience/giad025

Table of contents: - About DivBrowse - Installation - Try out DivBrowse - Screenshots - Usage workflow concept - Architecture


About DivBrowse

DivBrowse is a web application for interactive exploration and analysis of very large SNP matrices.

It offers a novel approach for interactive visualization and analysis of genomic diversity data and optionally also gene annotation data. The use of standard file formats for data input supports interoperability and seamless deployment of application instances based on established bioinformatics pipelines. The possible integration into 3rd-party web applications supports interoperability and reusability.

The integrated ad-hoc calculation of variant summary statistics and principal component analysis enables the user to perform interactive analysis of population structure for single genetic features like genes, exons and promoter regions. Data interoperability is achieved by the possibility to export genomic diversity data for genomic regions of interest in standardized VCF files.

Installation

The installation via pip or container images is described in the documentation: https://divbrowse.readthedocs.io/en/stable/installation.html

Try out DivBrowse

If you want to test DivBrowse please visit the demo instances listed here: https://divbrowse.ipk-gatersleben.de/#demo-instances

Screenshots

DivBrowse GUI

Usage workflow concept

Usage workflow concept

Architecture

Architecture

Owner

  • Name: IPK Gatersleben - Bioinformatics and Information Technology
  • Login: IPK-BIT
  • Kind: organization
  • Location: Germany

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  DivBrowse - interactive visualization and
  exploratory data analysis of variant call matrices
message: >-
  If you use this software, please cite it using the
  metadata from this file.
preferred-citation:
  authors:
    - given-names: Patrick
      family-names: König
      email: koenig@ipk-gatersleben.de
      orcid: 'https://orcid.org/0000-0002-8948-6793'
      affiliation: >-
        Leibniz Institute of Plant Genetics and Crop
        Plant Research (IPK) Gatersleben, 06466
        Seeland, Germany
    - given-names: Sebastian
      family-names: Beier
      orcid: 'https://orcid.org/0000-0002-2177-8781'
      affiliation: >-
        Leibniz Institute of Plant Genetics and Crop
        Plant Research (IPK) Gatersleben, 06466
        Seeland, Germany
      email: s.beier@fz-juelich.de
    - given-names: Martin
      family-names: Mascher
      email: mascher@ipk-gatersleben.de
      affiliation: >-
        Leibniz Institute of Plant Genetics and Crop
        Plant Research (IPK) Gatersleben, 06466
        Seeland, Germany
      orcid: 'https://orcid.org/0000-0001-6373-6013'
    - given-names: Nils
      family-names: Stein
      orcid: 'https://orcid.org/0000-0003-3011-8731'
      affiliation: >-
        Leibniz Institute of Plant Genetics and Crop
        Plant Research (IPK) Gatersleben, 06466
        Seeland, Germany
      email: stein@ipk-gatersleben.de
    - given-names: Matthias
      family-names: Lange
      email: lange@ipk-gatersleben.de
      orcid: 'https://orcid.org/0000-0002-4316-078X'
      affiliation: >-
        Leibniz Institute of Plant Genetics and Crop
        Plant Research (IPK) Gatersleben, 06466
        Seeland, Germany
    - given-names: Uwe
      family-names: Scholz
      orcid: 'https://orcid.org/0000-0001-6113-3518'
      email: scholz@ipk-gatersleben.de
      affiliation: >-
        Leibniz Institute of Plant Genetics and Crop
        Plant Research (IPK) Gatersleben, 06466
        Seeland, Germany
  title: DivBrowse - interactive visualization and exploratory data analysis of variant call matrices
  type: article
  doi: 10.1093/gigascience/giad025
  journal: GigaScience
  volume: 12
  year: 2023
type: software
authors:
  - given-names: Patrick
    family-names: König
    email: koenig@ipk-gatersleben.de
    orcid: 'https://orcid.org/0000-0002-8948-6793'
    affiliation: >-
      Leibniz Institute of Plant Genetics and Crop
      Plant Research (IPK) Gatersleben, 06466
      Seeland, Germany
  - given-names: Sebastian
    family-names: Beier
    orcid: 'https://orcid.org/0000-0002-2177-8781'
    affiliation: >-
      Leibniz Institute of Plant Genetics and Crop
      Plant Research (IPK) Gatersleben, 06466
      Seeland, Germany
    email: s.beier@fz-juelich.de
  - given-names: Martin
    family-names: Mascher
    email: mascher@ipk-gatersleben.de
    affiliation: >-
      Leibniz Institute of Plant Genetics and Crop
      Plant Research (IPK) Gatersleben, 06466
      Seeland, Germany
    orcid: 'https://orcid.org/0000-0001-6373-6013'
  - given-names: Nils
    family-names: Stein
    orcid: 'https://orcid.org/0000-0003-3011-8731'
    affiliation: >-
      Leibniz Institute of Plant Genetics and Crop
      Plant Research (IPK) Gatersleben, 06466
      Seeland, Germany
    email: stein@ipk-gatersleben.de
  - given-names: Matthias
    family-names: Lange
    email: lange@ipk-gatersleben.de
    orcid: 'https://orcid.org/0000-0002-4316-078X'
    affiliation: >-
      Leibniz Institute of Plant Genetics and Crop
      Plant Research (IPK) Gatersleben, 06466
      Seeland, Germany
  - given-names: Uwe
    family-names: Scholz
    orcid: 'https://orcid.org/0000-0001-6113-3518'
    email: scholz@ipk-gatersleben.de
    affiliation: >-
      Leibniz Institute of Plant Genetics and Crop
      Plant Research (IPK) Gatersleben, 06466
      Seeland, Germany
identifiers:
  - type: doi
    value: 10.1093/gigascience/giad025
    description: The DivBrowse paper on Oxford Academic GigaScience Journal.
  - type: url
    value: 'https://divbrowse.ipk-gatersleben.de'
    description: Project homepage
repository-code: 'https://github.com/IPK-BIT/divbrowse'
url: 'https://divbrowse.ipk-gatersleben.de/'
repository-artifact: 'https://pypi.org/project/divbrowse/'
doi: 10.1093/gigascience/giad025
journal: GigaScience
volume: 12
year: 2023
abstract: >-
  DivBrowse is a software for interactive
  visualization and analysis of the diversity of
  genomic variants. It uses VCF and GFF3 files as
  data input and consists of a web server written in
  Python and a GUI written in Javascript.
keywords:
  - genomics
  - data visualization
  - variation data
  - variant call format
  - biodiversity
license: MIT
#version: 1.0.1
date-released: '2023-04-21'

GitHub Events

Total
  • Watch event: 4
Last Year
  • Watch event: 4

Committers

Last synced: almost 2 years ago

All Time
  • Total Commits: 98
  • Total Committers: 1
  • Avg Commits per committer: 98.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 47
  • Committers: 1
  • Avg Commits per committer: 47.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Patrick König 3****g 98

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 9
  • Total pull requests: 0
  • Average time to close issues: 5 months
  • Average time to close pull requests: N/A
  • Total issue authors: 4
  • Total pull request authors: 0
  • Average comments per issue: 0.22
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • patrick-koenig (6)
  • lukasmueller (1)
  • juancresc (1)
  • langeipk (1)
Pull Request Authors
Top Labels
Issue Labels
enhancement (4) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 25 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 8
  • Total maintainers: 2
pypi.org: divbrowse

A web application for interactive visualization and analysis of genotypic variant matrices

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 25 Last month
Rankings
Dependent packages count: 7.3%
Stargazers count: 17.1%
Average: 19.5%
Dependent repos count: 22.1%
Forks count: 22.8%
Downloads: 28.1%
Maintainers (2)
matzel patrick-koenig
Last synced: 4 months ago

Dependencies

frontend/package.json npm
  • @rollup/plugin-commonjs ^17.0.0 development
  • @rollup/plugin-node-resolve ^11.0.0 development
  • @rollup/plugin-replace ^2.3.3 development
  • less ^3.11.1 development
  • postcss ^8.3.5 development
  • rollup ^2.3.4 development
  • rollup-plugin-css-only ^3.1.0 development
  • rollup-plugin-livereload ^2.0.0 development
  • rollup-plugin-root-import ^1.0.0 development
  • rollup-plugin-svelte ^7.0.0 development
  • rollup-plugin-terser ^7.0.0 development
  • svelte ^3.33.0 development
  • svelte-preprocess ^4.7.4 development
  • @sveltejs/svelte-virtual-list ^3.0.1
  • axios ^0.21.1
  • d3 ^5.16.0
  • dataframe-js ^1.4.4
  • fuse.js ^6.4.6
  • lodash ^4.17.15
  • plotly.js-dist ^1.54.7
  • sirv-cli ^1.0.0
  • svelte-inview ^1.0.0
  • svelte-moveable ^0.8.11
  • svelte-range-slider-pips ^1.7.0
  • svelte-simple-datatables ^0.1.25
  • svelte-simple-modal ^0.6.0
  • sveltejs-tippy ^3.0.0
  • tippy.js ^6.2.3
divbrowse/setup.py pypi
  • flask *
pyproject.toml pypi
  • sphinx ^4.0.2 develop
  • sphinx-autoapi ^1.6.0 develop
  • sphinx-click ^3.0.1 develop
  • sphinx_rtd_theme ^0.5.2 develop
  • bioblend ^0.16.0
  • click ^8.0.1
  • flask ^2.0.1
  • numpy ^1.21.1
  • pandas ^1.3.0
  • python ^3.9
  • pyyaml ^5.4.1
  • scikit-allel ^1.3.5
  • scikit-learn ^0.24.2
  • simplejson ^3.17.3
  • sphinx ^4.0.2
  • sphinx-autoapi ^1.6.0
  • sphinx-click ^3.0.1
  • sphinx_rtd_theme ^0.5.2
  • tables ^3.6.1
  • umap-learn ^0.5.2
  • waitress 2.1.2
  • zarr ^2.8.3
.github/workflows/publish-to-test-pypi.yml actions
  • actions/checkout master composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish master composite
environment.yml pypi