Data

Tools

Indexes

Applications

Experiments

Open Source Science

graphite

GRAPH Interaction from pathway Topological Environment

https://github.com/sales-lab/graphite

Science Score: 54.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic links in README
  • ✓
    Committers with academic emails
    1 of 16 committers (6.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (0.7%) to scientific vocabulary

Keywords

bioinformatics mirror pathway-analysis pathways r

Keywords from Contributors

bioconductor-package similarity-measurement similarity gene-sets gene functional-similarity bioconductor reproducibility targeted-learning computational-biology
Last synced: 6 months ago · JSON representation ·

Repository

GRAPH Interaction from pathway Topological Environment

Basic Info
  • Host: GitHub
  • Owner: sales-lab
  • Language: R
  • Default Branch: master
  • Size: 33.6 MB
Statistics
  • Stars: 8
  • Watchers: 1
  • Forks: 2
  • Open Issues: 2
  • Releases: 0
Topics
bioinformatics mirror pathway-analysis pathways r
Created over 8 years ago · Last pushed 10 months ago
Metadata Files
Citation

Owner

  • Name: Sales Lab
  • Login: sales-lab
  • Kind: organization

Citation (CITATION.cff) 

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.1.1
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "graphite" in publications use:'
type: software
license: AGPL-3.0-only
title: 'graphite: GRAPH Interaction from pathway Topological Environment'
version: 1.41.1
abstract: Graph objects from pathway topology derived from KEGG, Panther, PathBank,
  PharmGKB, Reactome SMPDB and WikiPathways databases.
authors:
- family-names: Sales
  given-names: Gabriele
  email: gabriele.sales@unipd.it
- family-names: Calura
  given-names: Enrica
  email: enrica.calura@gmail.com
- family-names: Romualdi
  given-names: Chiara
  email: chiara.romualdi@unipd.it
preferred-citation:
  type: article
  title: graphite - a Bioconductor package to convert pathway topology to gene network
  authors:
  - family-names: Sales
    given-names: Gabriele
  - family-names: Calura
    given-names: Enrica
  - family-names: Cavalieri
    given-names: Duccio
  - family-names: Romualdi
    given-names: Chiara
  journal: BMC Bioinformatics
  year: '2012'
  url: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-20
repository: https://bioconductor.org/
date-released: '2021-11-30'
contact:
- family-names: Sales
  given-names: Gabriele
  email: gabriele.sales@unipd.it
references:
- type: article
  title: metaGraphite - a new layer of pathway annotation to get metabolite networks
  authors:
  - family-names: Sales
    given-names: Gabriele
  - family-names: Calura
    given-names: Enrica
  - family-names: Romualdi
    given-names: Chiara
  journal: Bioinformatics
  year: '2018'
  url: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty719/5090451

GitHub Events

Total
  • Delete event: 5
  • Push event: 13
  • Create event: 2
Last Year
  • Delete event: 5
  • Push event: 13
  • Create event: 2

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 217
  • Total Committers: 16
  • Avg Commits per committer: 13.563
  • Development Distribution Score (DDS): 0.447
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Gabriele Sales g****s@g****m 120
Gabriele Sales g****s@u****t 34
Dan Tenenbaum d****a@f****g 22
Nitesh Turaga n****a@g****m 14
Enrica Calura e****a@g****m 5
Herve Pages h****s@f****g 5
Hervé Pagès h****s@f****g 3
J Wokaty j****y@s****u 2
Sonali Arora s****a@f****g 2
vobencha v****n@r****g 2
vobencha v****a@g****m 2
J Wokaty j****y 2
LiNk-NY m****9@g****m 1
Martin Morgan m****n@f****g 1
Nishant Gopalakrishnan n****k@f****g 1
Paul Shannon p****n@f****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 6 roswellpark.org: 1 sph.cuny.edu: 1 fredhutch.org: 1 unipd.it: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 5
  • Total pull requests: 0
  • Average time to close issues: 4 days
  • Average time to close pull requests: N/A
  • Total issue authors: 4
  • Total pull request authors: 0
  • Average comments per issue: 0.8
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
  • nfancy (2)
  • IsabellaLiFischer (1)
  • LetiLosa (1)
  • sonali8434 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 301,836 total
  • Total dependent packages: 11
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: graphite

GRAPH Interaction from pathway Topological Environment

  • Versions: 5
  • Dependent Packages: 11
  • Dependent Repositories: 0
  • Downloads: 301,836 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 2.7%
Downloads: 8.2%
Maintainers (1)
gabriele.sales@unipd.it
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.2 depends
  • methods * depends
  • AnnotationDbi * imports
  • graph >= 1.67.1 imports
  • graphics * imports
  • httr * imports
  • rappdirs * imports
  • rlang * imports
  • stats * imports
  • utils * imports
  • ALL * suggests
  • BiocStyle * suggests
  • R.rsp * suggests
  • RCy3 * suggests
  • SPIA >= 2.2 suggests
  • a4Preproc * suggests
  • checkmate * suggests
  • clipper * suggests
  • codetools * suggests
  • hgu133plus2.db * suggests
  • hgu95av2.db * suggests
  • impute * suggests
  • knitr * suggests
  • org.Hs.eg.db * suggests
  • parallel * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • topologyGSA >= 1.4.0 suggests