https://github.com/bioconductor-source/trnascanimport
Science Score: 26.0%
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○CITATION.cff file
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○.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (11.1%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: gpl-3.0
- Language: R
- Default Branch: devel
- Size: 313 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
tRNAscanImport 
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The default tRNAscan-SE (Lowe et el. 1997) output is formatted text
document containing text blocks per tRNA delimited by an empty line.
To access the information in a BioC context the conversion to a GRanges object
comes to mind. This task is performed by import.tRNAscanAsGRanges(), which uses
regular expressions to extract the information from the text blocks. The result
can be used directly or saved as gff3 file for further use.
Refer to the vignette for an example usage case.
Installation
The current version of the tRNAscanImport package is available from Bioconductor.
```{r} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("tRNAscanImport")
Load and attach thepackage
library("tRNAscanImport") ```
Literature
Depending on the development on tRNAscan-SE this might become redundant, since a gff3 export by tRNAscan-SE might resolve the conversion issue.
- Lowe, T.M.; Eddy, S.R.(1997): "tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence". Nucl. Acids Res. 25: 955-964. doi:10.1093/nar/25.5.955
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
GitHub Events
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Dependencies
- JamesIves/github-pages-deploy-action releases/v4 composite
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/upload-artifact master composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- JamesIves/github-pages-deploy-action releases/v4 composite
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/upload-artifact master composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- GenomicRanges * depends
- R >= 3.5 depends
- tRNA * depends
- BSgenome * imports
- BiocGenerics * imports
- Biostrings * imports
- GenomeInfoDb * imports
- IRanges * imports
- Rsamtools * imports
- S4Vectors * imports
- Structstrings * imports
- XVector * imports
- methods * imports
- rtracklayer * imports
- stringr * imports
- BSgenome.Scerevisiae.UCSC.sacCer3 * suggests
- BiocStyle * suggests
- ggplot2 * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests