tadar
R package for Transcriptome Analysis of Differential Allelic Representation
Science Score: 46.0%
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Found 1 DOI reference(s) in README -
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2 of 5 committers (40.0%) from academic institutions -
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Low similarity (11.4%) to scientific vocabulary
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Repository
R package for Transcriptome Analysis of Differential Allelic Representation
Basic Info
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
tadar 
tadar is a package designed to enable Transcriptome Analysis of Differential Allelic Representation (DAR).
DAR is parsimoniously defined as an unequal distribution of polymorphic loci between experimental sample groups; a situation likely to be encountered in RNA-seq experiments involving organisms that lack isogenicity. When unequally-represented polymorphic loci are also expression quantitative trait loci (eQTLs), differences in gene expression between groups can be incorrectly interpreted as a consequence of the experimental condition. DAR analysis is therefore recommended as a complementary technique alongside Differential Expression analysis. DAR analysis results in an easy-to-interpret value between 0 and 1 for each feature (e.g. gene) of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.
An example of the application of DAR analysis can be found in our manuscript.
Installation
BiocManager is recommended for the installation of this package.
r
install.packages("BiocManager")
BiocManager::install("tadar")
The development version of this package can also be installed from GitHub.
r
BiocManager::install("baerlachlan/tadar")
Owner
- Name: Lachlan Baer
- Login: baerlachlan
- Kind: user
- Location: Adelaide, South Australia
- Company: University of Adelaide
- Twitter: baerlachlan
- Repositories: 9
- Profile: https://github.com/baerlachlan
GitHub Events
Total
- Issues event: 1
- Issue comment event: 2
- Push event: 7
- Pull request event: 1
- Create event: 3
Last Year
- Issues event: 1
- Issue comment event: 2
- Push event: 7
- Pull request event: 1
- Create event: 3
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Lachlan Baer | b****n@g****m | 54 |
| J Wokaty | j****y@s****u | 4 |
| A Wokaty | a****y@s****u | 2 |
| J Wokaty | j****y@u****m | 2 |
| Stevie Ped | s****u@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 0
- Total pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: about 20 hours
- Total issue authors: 0
- Total 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
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: 2.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jonocarroll (1)
Pull Request Authors
- smped (3)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 4,519 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: tadar
Transcriptome Analysis of Differential Allelic Representation
- Homepage: https://github.com/baerlachlan/tadar
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/tadar/inst/doc/tadar.pdf
- License: GPL-3
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Latest release: 1.6.0
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- JamesIves/github-pages-deploy-action releases/v4 composite
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/upload-artifact master composite
- docker/build-push-action v4 composite
- docker/login-action v2 composite
- docker/setup-buildx-action v2 composite
- docker/setup-qemu-action v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- GenomicRanges * depends
- MatrixGenerics * imports
- S4Vectors * imports
- VariantAnnotation * imports
- covr * suggests
- knitr * suggests
- methods * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests