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ontoProc

https://github.com/vjcitn/ontoproc

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
    2 of 7 committers (28.6%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (2.3%) to scientific vocabulary

Keywords

bioinformatics genomics ontology

Keywords from Contributors

bioconductor-package derfinder rnaseq evolution flow-cytometry polyploidy image-analysis bioc gc-ms mass-spectrometry
Last synced: 6 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 5
  • Watchers: 2
  • Forks: 3
  • Open Issues: 9
  • Releases: 0
Topics
bioinformatics genomics ontology
Created over 4 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog

README.md

ontoProc -- an R package for working with multiple biomedical ontologies

In 2024, interfaces to owlready2 and bioregistry have been added to improve scope and functionality of package operations on OWL ontologies.

Includes the ctmarks app for examining cell types through ontological characterization

We also consider how to produce OBO stanzas for expanding existing ontologies

With this we can formally describe novel cell types (CL:X01 is an 'extended CL tag')

Owner

  • Name: Vince Carey
  • Login: vjcitn
  • Kind: user
  • Location: Boston

GitHub Events

Total
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 14
  • Create event: 1
Last Year
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 14
  • Create event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 102
  • Total Committers: 7
  • Avg Commits per committer: 14.571
  • Development Distribution Score (DDS): 0.235
Past Year
  • Commits: 8
  • Committers: 2
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.25
Top Committers
Name Email Commits
Vince Carey s****c@c****u 78
Nitesh Turaga n****a@g****m 14
Hervé Pagès h****s@f****g 2
J Wokaty j****y@s****u 2
shwetagopaul m****l@s****m 2
vobencha v****n@r****g 2
vobencha v****a@g****m 2
Committer Domains (Top 20 + Academic)
roswellpark.org: 1 shwetagopaul92.com: 1 sph.cuny.edu: 1 fredhutch.org: 1 channing.harvard.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 12
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 5
  • Total pull request authors: 4
  • Average comments per issue: 2.5
  • Average comments per pull request: 0.08
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 3 months
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.5
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • vjcitn (4)
  • februaryfang (1)
  • denvercal1234GitHub (1)
  • AlmogAngel (1)
Pull Request Authors
  • vjcitn (8)
  • vtarca7 (2)
  • stankiewicz565 (2)
  • Copilot (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 21,388 total
  • Total dependent packages: 3
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: ontoProc

processing of ontologies of anatomy, cell lines, and so on

  • Versions: 7
  • Dependent Packages: 3
  • Dependent Repositories: 0
  • Downloads: 21,388 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 18.3%
Downloads: 54.9%
Maintainers (1)
stvjc@channing.harvard.edu
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • ontologyIndex * depends
  • AnnotationHub * imports
  • Biobase * imports
  • BiocFileCache * imports
  • DT * imports
  • Rgraphviz * imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • dplyr * imports
  • graph * imports
  • igraph * imports
  • magrittr * imports
  • methods * imports
  • ontologyPlot * imports
  • shiny * imports
  • stats * imports
  • utils * imports
  • AnnotationDbi * suggests
  • BiocStyle * suggests
  • SingleCellExperiment * suggests
  • celldex * suggests
  • knitr * suggests
  • org.Hs.eg.db * suggests
  • org.Mm.eg.db * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/rworkflows.yml actions
  • neurogenomics/rworkflows master composite