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Open Source Science

https://github.com/alleninstitute/transcriptomic_clustering

improved clustering pipeline for transcriptomic data

https://github.com/alleninstitute/transcriptomic_clustering

Science Score: 36.0%

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
  • ✓
    Committers with academic emails
    5 of 8 committers (62.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

improved clustering pipeline for transcriptomic data

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • License: other
  • Language: Python
  • Default Branch: dev
  • Size: 447 KB
Statistics
  • Stars: 4
  • Watchers: 8
  • Forks: 2
  • Open Issues: 22
  • Releases: 0
Created over 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License Codeowners

README.md

transcriptomic_clustering

Clustering tools for transcriptomic data

Docker

singularity shell --cleanenv docker://njjai/tclust:0.1

Installing

For usage and installation instructions, see the install guide.

Contributing

We welcome contributions! Please see our contribution guide for more information. Thank you!

Level of Support

We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

GitHub Events

Total
  • Watch event: 1
  • Push event: 2
  • Pull request event: 4
  • Fork event: 1
Last Year
  • Watch event: 1
  • Push event: 2
  • Pull request event: 4
  • Fork event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 134
  • Total Committers: 8
  • Avg Commits per committer: 16.75
  • Development Distribution Score (DDS): 0.769
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Matt Aitken m****2@g****m 31
Sergey Gratiy s****g@a****g 26
gnayuy g****y@g****m 23
Zach Madigan z****n@a****g 23
jake.samson j****n@O****l 23
Nelson Johansen n****n@u****u 6
Wayne Wakeman w****w@a****g 1
Jake Samson j****n@i****g 1
Committer Domains (Top 20 + Academic)
alleninstitute.org: 3 ibs-bosiljkat-ux5.corp.alleninstitute.org: 1 ucdavis.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 0
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • dyuan1111 (9)
  • UCDNJJ (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

docker/hicat_on_terra_j_r/Dockerfile docker
  • us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base 0.0.12 build
docker/hicat_on_terra_j_r_master/Dockerfile docker
  • changkyul/hicat_on_terra_j_r latest build
requirements.txt pypi
  • Phenograph *
  • Welford *
  • anndata ==0.7.8
  • annoy *
  • click *
  • leidenalg ==0.8.4
  • networkx *
  • numpy *
  • pandas *
  • psutil *
  • python-louvain *
  • scanpy *
  • scikit-misc *
  • scipy >=1.7.0
  • six *
setup.py pypi
test_requirements.txt pypi
  • codecov ==2.1.12 test
  • coverage ==6.2.0 test
  • dictdiffer <1.0.0 test
  • flake8 >=1.5.0 test
  • mock >=1.0.1 test
  • moto >=1.3.14 test
  • numpydoc >=0.6.0 test
  • pep8 ==1.7.0 test
  • pylint >=1.5.4 test
  • pytest ==7.0.0 test
  • pytest-cov >=2.6.1 test
  • pytest-cover >=3.0.0 test
  • pytest-mock >=1.5.0 test
  • pytest-pep8 >=1.0.6 test
  • pytest-subtests ==0.6.0 test
  • pytest-xdist >=1.14 test
Dockerfile docker
  • python 3.8-bullseye build