packFinder

DOI: 10.18129/B9.bioc.packFinder    

de novo Annotation of Pack-TYPE Transposable Elements

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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 1.2.0
In Bioconductor since BioC 3.11 (R-4.0) (0.5 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_1.2.0.tar.gz
Windows Binary packFinder_1.2.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) packFinder_1.2.0.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

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