packFinder

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see packFinder.

de novo Annotation of Pack-TYPE Transposable Elements

Bioconductor version: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Genetics, SequenceMatching, Software

Version 1.6.0

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

Suggests biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle

Linking To

Enhances

Depends On Me

Imports 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_1.6.0.tar.gz

Windows Binary packFinder_1.6.0.zip

macOS 10.13 (High Sierra) packFinder_1.6.0.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 3.14 Source Archive