packFinder

de novo Annotation of Pack-TYPE Transposable Elements


Bioconductor version: Release (3.19)

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 (from within R, enter 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 PDF
NEWS Text

Details

biocViews Annotation, Genetics, SequenceMatching, Software
Version 1.16.0
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_1.16.0.tar.gz
Windows Binary (x86_64) packFinder_1.16.0.zip (64-bit only)
macOS Binary (x86_64) packFinder_1.16.0.tgz
macOS Binary (arm64) packFinder_1.16.0.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