packFinder

DOI: 10.18129/B9.bioc.packFinder    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see packFinder.

de novo Annotation of Pack-TYPE Transposable Elements

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	packFinder
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Genetics, SequenceMatching, Software
Version	1.8.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	GPL-2
Depends	R (>= 4.0.0)
Imports	Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors
LinkingTo
Suggests	biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/jackgisby/packFinder
BugReports	https://github.com/jackgisby/packFinder/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	packFinder_1.8.0.tar.gz
Windows Binary	packFinder_1.8.0.zip (64-bit only)
macOS Binary (x86_64)	packFinder_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/packFinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/packFinder
Package Short Url	https://bioconductor.org/packages/packFinder/
Package Downloads Report	Download Stats