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packFinder

This is the development version of packFinder; for the stable release version, see packFinder.

de novo Annotation of Pack-TYPE Transposable Elements


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.15.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
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Build Report Build Report

Package Archives

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

Source Package packFinder_1.15.0.tar.gz
Windows Binary packFinder_1.15.0.zip
macOS Binary (x86_64) packFinder_1.15.0.tgz
macOS Binary (arm64) packFinder_1.15.0.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