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Open Source Science

https://github.com/bioconductor/bsgenomeforge

Forge your own BSgenome data package

https://github.com/bioconductor/bsgenomeforge

Science Score: 26.0%

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
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.2%) to scientific vocabulary

Keywords

bioconductor-package core-package
Last synced: 6 months ago · JSON representation

Repository

Forge your own BSgenome data package

Basic Info
  • Host: GitHub
  • Owner: Bioconductor
  • Language: R
  • Default Branch: devel
  • Homepage:
  • Size: 202 KB
Statistics
  • Stars: 4
  • Watchers: 7
  • Forks: 3
  • Open Issues: 3
  • Releases: 0
Topics
bioconductor-package core-package
Created over 3 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog

README.md

BSgenomeForge is an R/Bioconductor package that provides a set of tools to forge BSgenome data packages. These new tools supersede the old seed-based tools from the BSgenome software package.

About BSgenome data packages

BSgenome data packages are one of the many types of annotation packages available in Bioconductor. They contain the genomic sequences, which comprise chromosome sequences and other DNA sequences, of a particular genome assembly for a given organism. For example BSgenome.Hsapiens.UCSC.hg19 is a BSgenome data package that contains the genomic sequences of the hg19 genome from UCSC. Users can easily and efficiently access the sequences, or portions of the sequences, stored in these packages, via a common API implemented in the BSgenome software package.

Bioconductor currently provides more than 100 BSgenome data packages, for more than 30 organisms. Most of them contain the genomic sequences of UCSC genomes (i.e. genomes supported by the UCSC Genome Browser) or NCBI assemblies. The packages are used in various Bioconductor workflows, as well as in man page examples and vignettes of other Bioconductor packages, typically in conjunction with tools available in the BSgenome and Biostrings software packages. New BSgenome data packages get added on a regular basis, based on user demand.

Useful links

  • BSgenome.Hsapiens.UCSC.hg19 landing page: https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19

  • List of BSgenome data packages available in Bioconductor: https://bioconductor.org/packages/release/BiocViews.html#___BSgenome

  • BSgenome software package landing page (with link to the old "How to forge a BSgenome data package" vignette): https://bioconductor.org/packages/BSgenome

  • BSgenome software package on GitHub: https://github.com/Bioconductor/BSgenome

  • Biostrings software package landing page: https://bioconductor.org/packages/Biostrings

  • GenomeInfoDb software package on GitHub: https://github.com/Bioconductor/GenomeInfoDb

Owner

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

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

GitHub Events

Total
  • Issues event: 2
  • Issue comment event: 4
  • Push event: 4
  • Pull request event: 1
  • Fork event: 2
  • Create event: 2
Last Year
  • Issues event: 2
  • Issue comment event: 4
  • Push event: 4
  • Pull request event: 1
  • Fork event: 2
  • Create event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 25
  • Total pull requests: 19
  • Average time to close issues: 13 days
  • Average time to close pull requests: 6 days
  • Total issue authors: 9
  • Total pull request authors: 5
  • Average comments per issue: 6.4
  • Average comments per pull request: 5.21
  • Merged pull requests: 18
  • 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: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • hpages (16)
  • junjunxy (1)
  • joegeorgeson (1)
  • ifanirene (1)
  • barracuda156 (1)
  • sadikmz (1)
  • ckuanglim85 (1)
  • JirkaMP (1)
  • vmurigneu (1)
  • kakopo (1)
Pull Request Authors
  • kakopo (15)
  • jeroen (2)
  • Simplecodez (1)
  • Priceless-P (1)
  • zhang-shilong (1)
Top Labels
Issue Labels
enhancement (7) outreachy dec2022 (2) good first issue (1) bug (1)
Pull Request Labels

Dependencies

DESCRIPTION cran
  • BSgenome * depends
  • BiocGenerics * depends
  • Biostrings * depends
  • GenomeInfoDb >= 1.33.17 depends
  • IRanges * depends
  • R >= 4.2.0 depends
  • S4Vectors * depends
  • methods * depends
  • Biobase * imports
  • rtracklayer * imports
  • stats * imports
  • utils * imports
  • BiocStyle * suggests
  • GenomicFeatures * suggests
  • GenomicRanges * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
inst/pkgtemplates/NCBI_BSgenome_datapkg/DESCRIPTION cran
  • BSgenome >= 1.66.1 depends
  • GenomeInfoDb >= 1.34.9 depends
  • R >= 4.2.0 depends
  • BSgenomeForge * suggests
inst/pkgtemplates/UCSC_BSgenome_datapkg/DESCRIPTION cran
  • BSgenome >= 1.66.1 depends
  • GenomeInfoDb >= 1.34.9 depends
  • R >= 4.2.0 depends
  • BSgenomeForge * suggests