Science Score: 46.0%
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 -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: nature.com -
✓Committers with academic emails
1 of 7 committers (14.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.9%) to scientific vocabulary
Keywords from Contributors
Repository
R wrapper around the hisat2 aligner.
Basic Info
- Host: GitHub
- Owner: fmicompbio
- License: gpl-3.0
- Language: C++
- Default Branch: devel
- Size: 13.9 MB
Statistics
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Rhisat2
The Rhisat2 R package provides an R interface to the hisat2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.
Source code
Rhisat2 v1.19.1 and newer
To allow compilation also on Linux aarch64, the Makefile obtained from hisat2 was adapted to exclude unsupported flags (-m64 and -msse2) on this platform. In addition, the mask2iupac array was converted from a char to a signed char. See here for the precise changes.
Rhisat2 v1.13.1 and newer
In Rhisat2 v1.13.1 and onwards, hisat2 was updated to v2.2.1, which was obtained from https://github.com/DaehwanKimLab/hisat2/releases on July 27, 2022.
Furthermore, Rhisat2 now includes parts of the SIMD Everywhere header library (https://github.com/simd-everywhere/simde) to support compilation on arm64, based on the implementation by Michael R. Crusoe crusoe@debian.org for the hisat2 (2.2.1-3) debian package (simde patch in http://deb.debian.org/debian/pool/main/h/hisat2/hisat2_2.2.1-3.debian.tar.xz, also forwarded in https://github.com/DaehwanKimLab/hisat2/pull/251).
Rhisat2 versions up to v1.13.0
The source code for hisat2 v2.1.0 was obtained from https://ccb.jhu.edu/software/hisat2/index.shtml on October 17, 2018.
Based on the discussion at https://github.com/BenLangmead/bowtie2/issues/81, the following small modification was made to allow compilation:
In the file src/aligner_result.cpp, line 1267
flag > 0
was replaced by
flag[0] != '\0'
Owner
- Login: fmicompbio
- Kind: user
- Repositories: 17
- Profile: https://github.com/fmicompbio
GitHub Events
Total
- Watch event: 1
- Push event: 14
- Create event: 2
Last Year
- Watch event: 1
- Push event: 14
- Create event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Charlotte Soneson | c****n@g****m | 128 |
| mbstadler | s****l@g****m | 18 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 4 |
| Hervé Pagès | h****b@g****m | 2 |
| Charlotte Soneson | c****e@f****h | 2 |
| J Wokaty | j****y | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 1
- Total pull requests: 5
- Average time to close issues: about 1 month
- Average time to close pull requests: 4 days
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 5.0
- Average comments per pull request: 1.4
- Merged pull requests: 5
- 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
Top Authors
Issue Authors
- bbarthold (1)
Pull Request Authors
- csoneson (5)
- mbstadler (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 29,848 total
- Total dependent packages: 3
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: Rhisat2
R Wrapper for HISAT2 Aligner
- Homepage: https://github.com/fmicompbio/Rhisat2
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/Rhisat2/inst/doc/Rhisat2.pdf
- License: GPL-3
-
Latest release: 1.24.0
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.6 depends
- GenomicFeatures * imports
- GenomicRanges * imports
- SGSeq * imports
- methods * imports
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- grimbough/bioc-actions/build-install-check v1 composite
- grimbough/bioc-actions/run-BiocCheck v1 composite
- grimbough/bioc-actions/setup-bioc v1 composite
- r-lib/actions/setup-pandoc v2 composite
- github-pages >= 0
- jekyll-feed >= 0
- jemoji >= 0