packFinder
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see packFinder.
de novo Annotation of Pack-TYPE Transposable Elements
Bioconductor version: 3.12
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)).
Author: Jack Gisby [aut, cre], Marco Catoni [aut]
Maintainer: Jack Gisby <jackgisby at gmail.com>
citation("packFinder")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("packFinder")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("packFinder")| packFinder | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Genetics, SequenceMatching, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | GPL-2 |
| Depends | R (>= 4.0.0) |
| Imports | Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors |
| System Requirements | |
| URL | https://github.com/jackgisby/packFinder |
| Bug Reports | https://github.com/jackgisby/packFinder/issues |
See More
| Suggests | biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | packFinder_1.2.0.tar.gz |
| Windows Binary | packFinder_1.2.0.zip |
| macOS 10.13 (High Sierra) | packFinder_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/packFinder |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/packFinder |
| Bioc Package Browser | https://code.bioconductor.org/browse/packFinder/ |
| Package Short Url | https://bioconductor.org/packages/packFinder/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |