packFinder
A package for the de novo discovery of pack-TYPE transposons
Science Score: 33.0%
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
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○.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
Links to: ncbi.nlm.nih.gov -
✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.4%) to scientific vocabulary
Keywords
Repository
A package for the de novo discovery of pack-TYPE transposons
Statistics
- Stars: 7
- Watchers: 1
- Forks: 1
- Open Issues: 1
- Releases: 0
Topics
Metadata Files
README.md
packFinder 
A package for the de novo discovery of Pack-TYPE transposons. Transposons are detected in DNA sequences based on conserved terminal inverted repeat sequences and presence of terminal site duplications. packFinder allows users to search a given Genome for Pack-TYPE transposons with minimal input and setup. For a more in-depth explanation, see our paper in PLOS Genetics.
Installation
packFinder is available from the Bioconductor project. With R >=4.0.0 installed, the following code can be used to install the package:
```
if (!require("BiocManager"))
install.packages("BiocManager")
BiocManager::install("packFinder") ```
In order to use the functions packClust and packAlign, the VSEARCH command line tool must be installed. For Linux and MacOS systems, correct installation of VSEARCH should allow users to use all functions within packFinder; for windows users, the absolute path to the VSEARCH executable file must be specified when calling packFinder clustering and alignment functions. See the vignette, documentation or the VSEARCH github for further information.
Additionally, utilites are provided with the package for the functional annotation of internal transposon sequences using BLAST+; this application can be installed from NCBI.
Using packFinder
The packFinder vignette includes a full walkthrough of the package. To get started quickly, it is easiest to download a genome of interest using the biomartr package and follow the steps outlined in the vignette.
Citation
If you use packFinder in your work, please cite the following publication:
Gisby, J. S. & Catoni, M. (2022) The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution. PLOS Genetics 18(2): e1010078.
Owner
- Name: Jack Gisby
- Login: jackgisby
- Kind: user
- Location: London
- Company: Imperial College London
- Twitter: jack_gisby
- Repositories: 4
- Profile: https://github.com/jackgisby
PhD candidate applying and developing data science approaches to investigate disease.
GitHub Events
Total
- Issues event: 1
- Watch event: 2
- Issue comment event: 1
Last Year
- Issues event: 1
- Watch event: 2
- Issue comment event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| jackgisby | 4****y | 170 |
| Jack Gisby | j****y@g****m | 34 |
| Nitesh Turaga | n****a@g****m | 10 |
| Jack Gisby (MSci Biochem w Prof Pla FT) | J****3@s****k | 3 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 1
- Total pull requests: 16
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.0
- Merged pull requests: 16
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- epi-lhe (1)
Pull Request Authors
- jackgisby (16)
Top Labels
Issue Labels
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Packages
- Total packages: 1
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Total downloads:
- bioconductor 8,874 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: packFinder
de novo Annotation of Pack-TYPE Transposable Elements
- Homepage: https://github.com/jackgisby/packFinder
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/packFinder/inst/doc/packFinder.pdf
- License: GPL-2
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Latest release: 1.20.0
published 10 months ago