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immunedb

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

https://github.com/arosenfeld/immunedb

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 4 committers (75.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.1%) to scientific vocabulary

Keywords

bioinformatics database immunology python
Last synced: 6 months ago · JSON representation

Repository

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

Basic Info
  • Host: GitHub
  • Owner: arosenfeld
  • License: other
  • Language: Python
  • Default Branch: master
  • Homepage: http://immunedb.com
  • Size: 15 MB
Statistics
  • Stars: 21
  • Watchers: 8
  • Forks: 11
  • Open Issues: 13
  • Releases: 0
Topics
bioinformatics database immunology python
Created over 11 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog Contributing License

README.md

ImmuneDB

Build Status Documentation Status codecov PyPI Docker Pulls

ImmuneDB is a Python module that facilitates efficient storage and analysis of high-throughput B- and T-cell sequence data.

Documentation

Installation and usage instructions can be found at immunedb.com

Support

Basic questions regarding installing and running ImmuneDB can be emailed to aaron.rosenfeld@pennmedicine.upenn.edu. Bugs and feature requests should be submitted as Issues. I try to respond to both within 2 business days if possible.

Citing

If you use ImmuneDB, please cite the tool as:

Rosenfeld, A. M., Meng, W., Luning Prak, E. T., Hershberg, U., ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data. Frontiers in Immunology 9 (2018).

ImmuneDB was originally announced previously in:

Rosenfeld, A. M., Meng, W., Luning Prak, E. T., Hershberg, U., ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data, Bioinformatics 33 (2016), no. 2, 292–293.

Owner

  • Name: Aaron Rosenfeld
  • Login: arosenfeld
  • Kind: user
  • Company: @PennHIC

GitHub Events

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

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 1,185
  • Total Committers: 4
  • Avg Commits per committer: 296.25
  • Development Distribution Score (DDS): 0.119
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Aaron Rosenfeld a****4@d****u 1,044
Aaron Rosenfeld a****d@p****u 94
Aaron Rosenfeld a****d 36
GregorySchwartz g****z@d****u 11
Committer Domains (Top 20 + Academic)
drexel.edu: 2 pennmedicine.upenn.edu: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 93
  • Total pull requests: 10
  • Average time to close issues: 7 months
  • Average time to close pull requests: over 1 year
  • Total issue authors: 12
  • Total pull request authors: 2
  • Average comments per issue: 0.89
  • Average comments per pull request: 1.3
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 8
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • arosenfeld (81)
  • aurelBZH (2)
  • Liamck (1)
  • areensh (1)
  • Elyes88 (1)
  • bcorrie (1)
  • ajulienla (1)
  • BlingArida (1)
  • linquynus (1)
  • haoqing12 (1)
  • azuretimm (1)
  • cornelius-agrippa (1)
Pull Request Authors
  • dependabot[bot] (15)
  • areensh (3)
Top Labels
Issue Labels
enhancement (48) bug (32) wontfix (13) duplicate (1) invalid (1)
Pull Request Labels
dependencies (15)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 82 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 29
  • Total maintainers: 1
pypi.org: immunedb

A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

  • Versions: 29
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 82 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 10.9%
Stargazers count: 13.6%
Average: 14.6%
Downloads: 16.6%
Dependent repos count: 21.7%
Maintainers (1)
arosenfeld
Last synced: 7 months ago

Dependencies

.github/workflows/container.yaml actions
  • actions/checkout v3 composite
  • mr-smithers-excellent/docker-build-push v6 composite
requirements.txt pypi
  • PyMySQL ==0.9.3
  • SQLAlchemy ==1.3.3
  • biopython ==1.73
  • bottle ==0.12.16
  • coloredlogs ==10.0
  • ete3 ==3.1.1
  • eventlet ==0.24.1
  • gunicorn ==19.9.0
  • matplotlib ==3.3.4
  • numpy ==1.19.5
  • pandas ==1.1.5
  • scipy ==1.5.4
  • seaborn ==0.9.0
  • six ==1.11.0
setup.py pypi
  • sphinxcontrib-websupport *
Dockerfile docker
  • ubuntu 20.04 build