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SeqVarTools

An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis

https://github.com/smgogarten/seqvartools

Science Score: 23.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    5 of 15 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.4%) to scientific vocabulary

Keywords from Contributors

bioconductor-package bioinformatics core-package metabolomics mass-spectrometry bioconductor gene cleavage digest peptides
Last synced: 10 months ago · JSON representation

Repository

An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis

Basic Info
Statistics
  • Stars: 3
  • Watchers: 4
  • Forks: 3
  • Open Issues: 1
  • Releases: 0
Created almost 9 years ago · Last pushed almost 2 years ago
Metadata Files
Readme

README.md

SeqVarTools

An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.

Bioconductor

http://www.bioconductor.org/packages/release/bioc/html/SeqVarTools.html

Installation

R if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("SeqVarTools")

Owner

  • Name: Stephanie M. Gogarten
  • Login: smgogarten
  • Kind: user
  • Location: Seattle, WA
  • Company: Department of Biostatistics, University of Washington

GitHub Events

Total
Last Year

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 173
  • Total Committers: 15
  • Avg Commits per committer: 11.533
  • Development Distribution Score (DDS): 0.618
Past Year
  • Commits: 4
  • Committers: 2
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
Stephanie M. Gogarten s****s@u****u 66
Stephanie Gogarten s****s@u****u 39
Nitesh Turaga n****a@g****m 14
Dan Tenenbaum d****a@f****g 12
smgogarten s****n@v****a 10
Adrienne Stilp a****p@u****u 7
Herve Pages h****s@f****g 4
J Wokaty j****y@s****u 4
Xiuwen Zheng z****x@u****u 4
J Wokaty j****y 4
Hervé Pagès h****s@f****g 2
Sonali Arora s****a@f****g 2
vobencha v****n@r****g 2
vobencha v****a@g****m 2
Marc Carlson m****n@f****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 4 u.washington.edu: 2 uw.edu: 2 roswellpark.org: 1 fredhutch.org: 1 sph.cuny.edu: 1

Issues and Pull Requests

Last synced: almost 2 years ago

All Time
  • Total issues: 6
  • Total pull requests: 1
  • Average time to close issues: 10 days
  • Average time to close pull requests: less than a minute
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 1.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: 7 days
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gustavahlberg (2)
  • smgogarten (2)
  • gtollefson (1)
  • amstilp (1)
Pull Request Authors
  • smgogarten (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 72,681 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: SeqVarTools

Tools for variant data

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 72,681 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 4.6%
Downloads: 13.8%
Maintainers (1)
sdmorris@uw.edu
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • SeqArray * depends
  • Biobase * imports
  • BiocGenerics * imports
  • GWASExactHW * imports
  • GenomicRanges * imports
  • IRanges * imports
  • Matrix * imports
  • S4Vectors * imports
  • data.table * imports
  • gdsfmt * imports
  • grDevices * imports
  • graphics * imports
  • logistf * imports
  • methods * imports
  • stats * imports
  • BiocStyle * suggests
  • RUnit * suggests
  • stringr * suggests