packFinder
de novo Annotation of Pack-TYPE Transposable Elements
Bioconductor version: Release (3.20)
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 "4.4") 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 | 1.18.0 |
In Bioconductor since | BioC 3.11 (R-4.0) (4.5 years) |
License | GPL-2 |
Depends | R (>= 4.1.0) |
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_1.18.0.tar.gz |
Windows Binary (x86_64) | packFinder_1.18.0.zip (64-bit only) |
macOS Binary (x86_64) | packFinder_1.18.0.tgz |
macOS Binary (arm64) | packFinder_1.17.0.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 |