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VariantExperiment

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

https://github.com/bioconductor/variantexperiment

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 8 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (2.5%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene ontology proteomics annotation genomics u24ca289073 mutations data-structure copynumber
Last synced: 10 months ago · JSON representation

Repository

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

Basic Info
  • Host: GitHub
  • Owner: Bioconductor
  • Language: R
  • Default Branch: devel
  • Homepage:
  • Size: 2.96 MB
Statistics
  • Stars: 1
  • Watchers: 10
  • Forks: 0
  • Open Issues: 2
  • Releases: 0
Created over 8 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

VariantExperiment

VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data are saved in GDSArray objects. The annotation data for features/samples are saved in DelayedDataFrame format with mono-dimensional GDSArray in each column. The on-disk representation of both assay data and annotation data achieves on-disk reading and processing and saves memory space significantly. The interface of RangedSummarizedExperiment data format enables easy and common manipulations for high-throughput genetic/genomic data with common SummarizedExperiment metaphor in R and Bioconductor.

Owner

  • Name: Bioconductor
  • Login: Bioconductor
  • Kind: organization

Software for the analysis and comprehension of high-throughput genomic data

GitHub Events

Total
  • Push event: 2
  • Create event: 2
Last Year
  • Push event: 2
  • Create event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 190
  • Total Committers: 8
  • Avg Commits per committer: 23.75
  • Development Distribution Score (DDS): 0.211
Past Year
  • Commits: 7
  • Committers: 3
  • Avg Commits per committer: 2.333
  • Development Distribution Score (DDS): 0.429
Top Committers
Name Email Commits
Qian Liu q****7@b****u 150
Martin Morgan m****n@r****g 18
Nitesh Turaga n****a@g****m 12
J Wokaty j****y@s****u 4
Liu q****6@C****l 2
J Wokaty j****y 2
Qian Liu l****c@g****m 1
Hervé Pagès h****s@f****g 1
Committer Domains (Top 20 + Academic)
fredhutch.org: 1 sph.cuny.edu: 1 roswellpark.org: 1 buffalo.edu: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 5
  • Total pull requests: 0
  • Average time to close issues: 5 months
  • Average time to close pull requests: N/A
  • Total issue authors: 4
  • Total pull request authors: 0
  • Average comments per issue: 10.4
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • Liubuntu (2)
  • waddella (1)
  • lawremi (1)
  • cmatKhan (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 8,720 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: VariantExperiment

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 8,720 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 19.8%
Average: 24.7%
Stargazers count: 29.0%
Downloads: 74.7%
Maintainers (1)
Qian.Liu@roswellpark.org
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • GenomicRanges * depends
  • R >= 3.6.0 depends
  • S4Vectors >= 0.21.24 depends
  • SummarizedExperiment >= 1.13.0 depends
  • Biostrings * imports
  • DelayedArray * imports
  • DelayedDataFrame >= 1.6.0 imports
  • GDSArray >= 1.11.1 imports
  • IRanges * imports
  • SNPRelate * imports
  • SeqArray * imports
  • gdsfmt * imports
  • methods * imports
  • stats * imports
  • tools * imports
  • utils * imports
  • BiocStyle * suggests
  • knitr * suggests
  • markdown * suggests
  • rmarkdown * suggests
  • testthat * suggests