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ocat

https://github.com/bowang-lab/ocat

Science Score: 49.0%

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
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.2%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: bowang-lab
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Size: 1.03 GB
Statistics
  • Stars: 18
  • Watchers: 2
  • Forks: 3
  • Open Issues: 2
  • Releases: 3
Created over 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

OCAT - One Cell At A Time

OCAT provides a fast and memory-efficient framework for analyzing and integrating large-scale scRNA-seq data. Our paper is now published in Genome Biology!!!

Check out rOCAT to use OCAT in R!

:heavyplussign: Method

OCAT constructs sparse representation of cell features through ghost cells in the datasets. These ghost cells serve as bridges to inform on cell-cell similarity between the original cells. With the sparse features extracted, OCAT provides an efficient framework for cell type clustering and dataset integration that achieves state-of-the-art performance.


:triangular_ruler: Requirements and Installation

  • Linux/Unix
  • Python 3.7

Install OCAT package from PyPI. Pre-installation of Numpy and Cython required. bash $ pip install numpy $ pip install OCAT

:heavyplussign: Tutorials

Owner

  • Name: WangLab @ U of T
  • Login: bowang-lab
  • Kind: organization
  • Location: 190 Elizabeth St, Toronto, ON M5G 2C4 Canada

BoWang's Lab at University of Toronto

GitHub Events

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

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 279
  • Total Committers: 3
  • Avg Commits per committer: 93.0
  • Development Distribution Score (DDS): 0.369
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Lin Zhang 5****c 176
ChloeXWang x****g@m****a 79
Chong c****o@m****a 24
Committer Domains (Top 20 + Academic)
mail.utoronto.ca: 1 mail.mcgill.ca: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 4
  • Total pull requests: 5
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 2 minutes
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 1.75
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • 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
  • Yuxin-Cui (1)
  • Sayyam-Shah (1)
  • martina811 (1)
  • JuliaChristiaanse (1)
Pull Request Authors
  • shaochon (5)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 16 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 79
  • Total maintainers: 2
pypi.org: ocat

A new single-cell analytics framework

  • Versions: 79
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 16 Last month
Rankings
Dependent packages count: 10.0%
Stargazers count: 14.2%
Average: 16.8%
Forks count: 16.9%
Downloads: 21.0%
Dependent repos count: 21.7%
Maintainers (2)
chong.shao ChloeXWang
Last synced: 7 months ago

Dependencies

OCAT.egg-info/requires.txt pypi
  • cython *
  • matplotlib *
  • networkX *
  • numpy >=1.17.2
  • pandas *
  • scikit-learn >=0.21.3
  • scipy >=1.3.1
  • seaborn *
  • umap-learn *
setup.py pypi
  • cython *
  • matplotlib *
  • networkX *
  • numpy >=1.17.2
  • pandas *
  • scikit-learn >=0.21.3
  • scipy >=1.3.1
  • seaborn *
  • umap-learn *