SynExtend

DOI: 10.18129/B9.bioc.SynExtend    

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

Tools for Working With Synteny Objects

Bioconductor version: 3.15

Shared order between genomic sequences provide a great deal of information. Synteny objects produced by the R package DECIPHER provides quantitative information about that shared order. SynExtend provides tools for extracting information from Synteny objects.

Author: Nicholas Cooley [aut, cre] , Aidan Lakshman [aut, ctb] , Adelle Fernando [ctb], Erik Wright [aut]

Maintainer: Nicholas Cooley <npc19 at pitt.edu>

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SynExtend")

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("SynExtend")

 

PDF	R Script	UsingSynExtend
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, ComparativeGenomics, DataImport, Genetics, Software
Version	1.8.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	GPL-3
Depends	R (>= 4.1.0), DECIPHER(>= 2.20.0)
Imports	methods, Biostrings, S4Vectors, IRanges, utils, stats, parallel, graphics, grDevices
LinkingTo
Suggests	BiocStyle, knitr, rtracklayer, igraph, markdown, rmarkdown
SystemRequirements
Enhances
URL
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	SynExtend_1.8.0.tar.gz
Windows Binary	SynExtend_1.8.0.zip
macOS Binary (x86_64)	SynExtend_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SynExtend
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SynExtend
Package Short Url	https://bioconductor.org/packages/SynExtend/
Package Downloads Report	Download Stats