Science Score: 49.0%
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
Found 9 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
3 of 9 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.2%) to scientific vocabulary
Keywords from Contributors
Repository
Analysis of transposable elements
Basic Info
- Host: GitHub
- Owner: rcastelo
- Language: R
- Default Branch: devel
- Size: 12.8 MB
Statistics
- Stars: 12
- Watchers: 2
- Forks: 2
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
atena: analysis of transposable elements in R and Bioconductor
Current Bioconductor build status
- release 
- development 
The atena package provides access from R/Bioconductor to the following
methods for the quantification of transposable element (TE) expression:
Jin Y et al. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics. 2015;31(22):3593-3599. DOI: 10.1093/bioinformatics/btv422.
Tokuyama M et al. ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses. PNAS. 2018;115(50):12565-12572. DOI: 10.1073/pnas.1814589115.
Bendall et al. Telescope: characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLOS Comp. Biol. 2019;15(9):e1006453. DOI: 10.1371/journal.pcbi.1006453.
Installation
atena has been submitted to Bioconductor.
To install the release version of this package please go to its package release landing page at https://bioconductor.org/packages/atena and follow the instructions there to install it.
This github repository contains the development version of the
R/Bioconductor package atena. This version is unstable and should be used
only to test new features. To install the development version you first need to
install the
development version of Bioconductor
and then type the following line from the R shell:
r
BiocManager::install("atena", version="devel")
Alternatively, you can directly install it from this GitHub repo as follows:
BiocManager::install("rcastelo/atena")
Questions, bug reports and issues
For questions and bug reports regarding the release version of atena please use the Bioconductor support site. For bug reports and issues regarding this development version of atena please use the GitHub issues tab at the top-left of this page.
Contributing
Contributions to the software codebase of atena are welcome as long as contributors abide to the terms of the Bioconductor Contributor Code of Conduct. If you want to contribute to the development of GenomicScores please open an issue to start discussing your suggestion or, in case of a bugfix or a straightforward feature, directly a pull request.
Funding
This software project is supported in part by the Spanish Ministry of Science, Innovation and Universities.
Owner
- Name: Robert Castelo
- Login: rcastelo
- Kind: user
- Location: Barcelona
- Company: Universitat Pompeu Fabra
- Website: https://functionalgenomics.upf.edu
- Twitter: robertclab
- Repositories: 15
- Profile: https://github.com/rcastelo
biostatistics, machine learning, genetics, genomics, R/Bioconductor
GitHub Events
Total
- Watch event: 5
- Issue comment event: 6
- Push event: 5
- Create event: 2
Last Year
- Watch event: 5
- Issue comment event: 6
- Push event: 5
- Create event: 2
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| beacalvo | b****6@g****m | 250 |
| Robert Castelo | r****o@u****u | 43 |
| pablo-rodr-bio2 | p****2@g****m | 15 |
| [rcastelo] | [****o@u****] | 14 |
| Beatriz Calvo Serra | 4****o | 7 |
| J Wokaty | j****y@s****u | 4 |
| Nitesh Turaga | n****a@g****m | 4 |
| J Wokaty | j****y | 4 |
| Peter Hickey | p****y@g****m | 3 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 3
- Total pull requests: 5
- Average time to close issues: 7 days
- Average time to close pull requests: 9 days
- Total issue authors: 2
- Total pull request authors: 3
- Average comments per issue: 4.33
- Average comments per pull request: 0.4
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: 19 days
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 6.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- martin-g (2)
- biga94 (1)
Pull Request Authors
- pablo-rodr-bio2 (3)
- beacalvo (1)
- PeteHaitch (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 10,231 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: atena
Analysis of Transposable Elements
- Homepage: https://github.com/rcastelo/atena
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/atena/inst/doc/atena.pdf
- License: Artistic-2.0
-
Latest release: 1.14.1
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.1 depends
- SummarizedExperiment * depends
- AnnotationHub * imports
- BiocGenerics * imports
- BiocParallel * imports
- GenomeInfoDb * imports
- GenomicAlignments * imports
- GenomicRanges * imports
- IRanges * imports
- Matrix * imports
- Rsamtools * imports
- S4Vectors * imports
- SQUAREM * imports
- matrixStats * imports
- methods * imports
- scales * imports
- sparseMatrixStats * imports
- stats * imports
- BiocStyle * suggests
- RUnit * suggests
- covr * suggests
- knitr * suggests
- rmarkdown * suggests
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite