packFinder
de novo Annotation of Pack-TYPE Transposable Elements
Bioconductor version: 3.24 · Package version: 1.25.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("packFinder")Details
| Maintainer | Jack Gisby <jackgisby@gmail.com> |
| Author | Jack Gisby [aut, cre] (ORCID: <https://orcid.org/0000-0003-0511-8123>), Marco Catoni [aut] (ORCID: <https://orcid.org/0000-0002-3258-2522>) |
| License | GPL-2 |
| URL | https://github.com/jackgisby/packFinder |
| Bug Reports | https://github.com/jackgisby/packFinder/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, Genetics, SequenceMatching, Software |
| Package Short Url | https://bioconductor.org/packages/packFinder/ |
Citation
From within R, enter citation("packFinder"):
Jack Gisby, Marco Catoni. packFinder: de novo Annotation of Pack-TYPE Transposable Elements. doi:10.18129/B9.bioc.packFinder, R package version 1.25.0, https://bioconductor.org/packages/packFinder.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | packFinder_1.25.0.tar.gz |
| Windows binary (x86_64) | packFinder_1.25.0.zip |
| macOS binary (arm64) | packFinder_1.25.0.tgz |
| macOS binary (x86_64) | packFinder_1.25.0.tgz |
Dependencies
Depends: R (>= 4.1.0)
Imports: Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors
Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle