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microhapdb

Portable database of microhaplotype marker and allele frequency data

https://github.com/bioforensics/microhapdb

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
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.2%) to scientific vocabulary

Keywords

bioinformatics forensics hacktoberfest microhaplotypes ngs
Last synced: 6 months ago · JSON representation

Repository

Portable database of microhaplotype marker and allele frequency data

Basic Info
Statistics
  • Stars: 10
  • Watchers: 2
  • Forks: 4
  • Open Issues: 1
  • Releases: 19
Topics
bioinformatics forensics hacktoberfest microhaplotypes ngs
Created over 7 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License Citation

README.md

MicroHapDB

MicroHapDB build status Install with bioconda BSD licensed

NBFAC, 2018-2025 https://github.com/bioforensics/microhapdb

MicroHapDB is a comprehensive catalog of human microhaplotype variation. The database integrates marker and population frequency data from numerous published research articles. Allele frequency estimates and allelic diversity statistics ($A_e$) are computed for 26 global populations so that markers can be ranked and evaluated for various applications.

MicroHapDB is managed as a community resource requiring minimal infrastructure to maintain: the entire contents of the database are distributed in plain text with each copy of MicroHapDB. The primary interface to MicroHapDB is through the console command line, which provides methods for browsing, searching, and filtering the database contents. Full programmatic access is available via a Python API. Alternatively, users can access the database tables directly using a spreadsheet program such as Microsoft Excel.

Binder

Installation

See this page for complete installation instructions. If this isn't your first rodeo, the commands below are provided as a quick reference.

conda install -c bioconda microhapdb pytest pytest --pyargs microhapdb --doctest-modules

Usage

MicroHapDB provides several methods to access the contents of a locally installed database. The MicroHapDB documentation includes a "Getting started" guide as well as a comprehensive reference for running MicroHapDB on the command line.

Citation

If you use this database, please cite our work.

Standage DS, Mitchell RN (2020) MicroHapDB: A Portable and Extensible Database of All Published Microhaplotype Marker and Frequency Data. Frontiers in Genetics 11:781, doi:10.3389/fgene.2020.00781.

MicroHapDB was created and is maintained by the Bioinformatics Group at the National Bioforensic Anaylsis Center (NBFAC).

Additional references are available on this page.

GitHub Events

Total
  • Create event: 7
  • Release event: 1
  • Issues event: 2
  • Watch event: 1
  • Delete event: 4
  • Issue comment event: 3
  • Push event: 24
  • Pull request review event: 2
  • Pull request review comment event: 5
  • Pull request event: 6
Last Year
  • Create event: 7
  • Release event: 1
  • Issues event: 2
  • Watch event: 1
  • Delete event: 4
  • Issue comment event: 3
  • Push event: 24
  • Pull request review event: 2
  • Pull request review comment event: 5
  • Pull request event: 6

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 139
  • Total Committers: 6
  • Avg Commits per committer: 23.167
  • Development Distribution Score (DDS): 0.561
Past Year
  • Commits: 54
  • Committers: 2
  • Avg Commits per committer: 27.0
  • Development Distribution Score (DDS): 0.333
Top Committers
Name Email Commits
Daniel Standage d****e@n****v 61
Daniel Standage d****e@g****m 57
Daniel Standage d****e@s****v 18
rnmitchell 5****l 1
danejo3 3****3 1
Ryan Berger 3****8 1
Committer Domains (Top 20 + Academic)
st.dhs.gov: 1 nbacc.dhs.gov: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 52
  • Total pull requests: 83
  • Average time to close issues: 4 months
  • Average time to close pull requests: 10 days
  • Total issue authors: 3
  • Total pull request authors: 4
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.93
  • Merged pull requests: 81
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: about 5 hours
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.33
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • standage (49)
  • vmevada102 (1)
  • danejo3 (1)
Pull Request Authors
  • standage (84)
  • rnmitchell (1)
  • RyanBerger98 (1)
  • danejo3 (1)
Top Labels
Issue Labels
datasources (19) enhancement (12) bug (11) testing (2)
Pull Request Labels
datasources (13) enhancement (10) refactoring (3) bug (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 63 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 14
  • Total maintainers: 1
pypi.org: microhapdb

Portable database of microhaplotype marker and allele frequency data

  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 63 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 16.8%
Average: 17.3%
Downloads: 18.7%
Stargazers count: 19.3%
Dependent repos count: 21.7%
Maintainers (1)
daniel.standage
Last synced: 6 months ago