Rbowtie

This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.

https://github.com/fmicompbio/rbowtie

Science Score: 36.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
Found 1 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
1 of 15 committers (6.7%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (9.3%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene genomics bioconductor bioinformatics proteomics core-package metabolomics looking-for-maintainer mass-spectrometry

Last synced: 10 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: fmicompbio
License: other
Language: C++
Default Branch: devel
Homepage: https://fmicompbio.github.io/Rbowtie/
Size: 7.72 MB

Statistics

Stars: 1
Watchers: 2
Forks: 0
Open Issues: 0
Releases: 0

Created over 7 years ago · Last pushed about 1 year ago

Metadata Files

Readme License

README.md

Rbowtie

The Rbowtie R package provides an R interface to the bowtie short-read aligner by Langmead et al. (2009), as well as to SpliceMap by Au et al. (2010). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index. These are used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.

Source code

The source code for bowtie v1.3.0 was obtained from https://github.com/BenLangmead/bowtie/archive/v1.3.0.tar.gz on November 2, 2020. The folders genomes, reads, doc, indexes and scripts were not included into the package to reduce its size.

Software status

Owner

Login: fmicompbio
Kind: user

Repositories: 17
Profile: https://github.com/fmicompbio

GitHub Events

Total

Delete event: 1
Issue comment event: 1
Push event: 2
Pull request event: 2
Create event: 3

Last Year

Delete event: 1
Issue comment event: 1
Push event: 2
Pull request event: 2
Create event: 3

Committers

Last synced: over 2 years ago

All Time

Total Commits: 169
Total Committers: 15
Avg Commits per committer: 11.267
Development Distribution Score (DDS): 0.538

Past Year

Commits: 9
Committers: 3
Avg Commits per committer: 3.0
Development Distribution Score (DDS): 0.444

Top Committers

Name	Email	Commits
mbstadler	s**l@g**m	78
Michael Stadler	M**r@f**h	26
Dan Tenenbaum	d**a@f**g	23
Nitesh Turaga	n**a@g**m	14
Anita Lerch	a**h@f**h	9
Herve Pages	h**s@f**g	5
vobencha	v**n@r**g	2
vobencha	v**a@g**m	2
Hervé Pagès	h**s@f**g	2
J Wokaty	j****y	2
J Wokaty	j**y@s**u	2
Martin Morgan	M**n@R**g	1
Nishant Gopalakrishnan	n**k@f**g	1
Hervé Pagès	h**b@g**m	1
Sonali Arora	s**a@f**g	1

Committer Domains (Top 20 + Academic)

fhcrc.org: 4 roswellpark.org: 2 fmi.ch: 2 sph.cuny.edu: 1 fredhutch.org: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time

Total issues: 0
Total pull requests: 4
Average time to close issues: N/A
Average time to close pull requests: about 1 hour
Total issue authors: 0
Total pull request authors: 2
Average comments per issue: 0
Average comments per pull request: 0.5
Merged pull requests: 4
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: about 5 hours
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 1.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

Pull Request Authors

mbstadler (3)
csoneson (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- bioconductor 79,688 total

Total dependent packages: 5
Total dependent repositories: 0
Total versions: 5
Total maintainers: 1

bioconductor.org: Rbowtie

R bowtie wrapper

Homepage: https://github.com/fmicompbio/Rbowtie
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/Rbowtie/inst/doc/Rbowtie.pdf
License: Artistic-2.0 | file LICENSE
Latest release: 1.48.0
published about 1 year ago

Versions: 5
Dependent Packages: 5
Dependent Repositories: 0
Downloads: 79,688 Total

Rankings

Dependent repos count: 0.0%

Dependent packages count: 0.0%

Average: 4.2%

Downloads: 12.5%

Maintainers (1)

michael.stadler@fmi.ch

Last synced: 11 months ago

Dependencies

DESCRIPTION cran

BiocStyle * suggests
knitr * suggests
parallel * suggests
rmarkdown * suggests
testthat * suggests

.github/workflows/build_and_check.yml actions

actions/cache v1 composite
actions/checkout v2 composite
actions/upload-artifact master composite
r-lib/actions/setup-pandoc master composite
r-lib/actions/setup-r master composite