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doppelgangR

Identify possibly duplicate samples in a list of ExpressionSets

https://github.com/waldronlab/doppelgangR

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
    3 of 18 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (1.9%) to scientific vocabulary

Keywords

bioconductor-package

Keywords from Contributors

gene genomics core-package u24ca289073 tumor-purity tumor-mutational-burden microbiome tumor-heterogeneity loh metabolomics
Last synced: 11 months ago · JSON representation

Repository

Identify possibly duplicate samples in a list of ExpressionSets

Basic Info
Statistics
  • Stars: 5
  • Watchers: 4
  • Forks: 4
  • Open Issues: 0
  • Releases: 0
Topics
bioconductor-package
Created about 13 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

doppelgangR

Identify possibly duplicate samples in a list of ExpressionSets. The main function is doppelgangR(), whose main input argument is a list of ExpressionSets. This function uses similarity of expression profiles, similarity of `phenoData, and matching of supposedly unique identifiers to find potential duplicate samples in the database.

Results from running doppelgangR on CRC, bladder, and ovarian on Dropbox.

For the manuscript vignette, visit https://github.com/waldronlab/doppelgangR_paper.

Owner

  • Name: Waldron Lab at the CUNY SPH
  • Login: waldronlab
  • Kind: organization
  • Email: Levi.Waldron@sph.cuny.edu
  • Location: New York, NY, USA

Software and educational materials from the Waldron lab for computational biostatistics at the CUNY SPH in New York City

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 9
  • Pull request review event: 2
  • Pull request event: 2
  • Fork event: 1
  • Create event: 2
Last Year
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 9
  • Pull request review event: 2
  • Pull request event: 2
  • Fork event: 1
  • Create event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 193
  • Total Committers: 18
  • Avg Commits per committer: 10.722
  • Development Distribution Score (DDS): 0.534
Past Year
  • Commits: 10
  • Committers: 3
  • Avg Commits per committer: 3.333
  • Development Distribution Score (DDS): 0.6
Top Committers
Name Email Commits
Levi Waldron l****h@g****m 90
Levi Waldron l****n@h****u 23
lima1 m****r@g****e 21
LiNk-NY m****9@g****m 16
Nitesh Turaga n****a@g****m 14
Herve Pages h****s@f****g 4
Dan Tenenbaum d****a@f****g 4
J Wokaty j****y@s****u 4
Fabio Da Col f****3@g****m 3
vobencha v****n@r****g 2
vobencha v****a@g****m 2
Hervé Pagès h****s@f****g 2
Levi Waldron l****1@S****) 2
J Wokaty j****y 2
lwaldron l****n@h****u 1
Kayla-Morrell k****l@r****g 1
Martin Morgan m****n@f****g 1
Xavier Robin x****b@x****e 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 3 roswellpark.org: 2 xavier.robin.name: 1 hunter.cuny.edu: 1 sc-538-43094.(none): 1 fredhutch.org: 1 sph.cuny.edu: 1 gmx.de: 1 hsph.harvard.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 19
  • Total pull requests: 3
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 3 days
  • Total issue authors: 5
  • Total pull request authors: 3
  • Average comments per issue: 1.21
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 7 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • lwaldron (15)
  • maddahi93 (1)
  • lima1 (1)
  • jwokaty (1)
  • reem-hassan (1)
Pull Request Authors
  • bd4everyone (2)
  • xrobin (1)
  • maddahi93 (1)
Top Labels
Issue Labels
enhancement (8) bug (5) wontfix (1) needs information (1)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 18,880 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: doppelgangR

Identify likely duplicate samples from genomic or meta-data

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 18,880 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 17.7%
Downloads: 53.2%
Maintainers (1)
lwaldron.research@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • Biobase * depends
  • BiocParallel * depends
  • R >= 3.5.0 depends
  • SummarizedExperiment * imports
  • digest * imports
  • grDevices * imports
  • graphics * imports
  • impute * imports
  • methods * imports
  • mnormt * imports
  • stats * imports
  • sva * imports
  • utils * imports
  • BiocStyle * suggests
  • curatedOvarianData * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/check.yml actions
  • actions/cache v4 composite
  • actions/checkout v3 composite