SynExtend

DOI: 10.18129/B9.bioc.SynExtend    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SynExtend.

Tools for Working With Synteny Objects

Bioconductor version: 3.12

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] , Adelle Fernando [ctb], Erik Wright [aut]

Maintainer: Nicholas Cooley <npc19 at pitt.edu>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	ExploreModelMatrix
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, ComparativeGenomics, DataImport, Genetics, Software
Version	1.2.0
In Bioconductor since	BioC 3.11 (R-4.0) (1 year)
License	GPL-3
Depends	R (>= 4.0.0), DECIPHER(>= 2.14.0), igraph (>= 1.2.4.1)
Imports	methods, Biostrings, S4Vectors, IRanges, utils, stats
LinkingTo
Suggests	knitr
SystemRequirements
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Depends On Me
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Build Report

Package Archives

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

Source Package	SynExtend_1.2.0.tar.gz
Windows Binary	SynExtend_1.2.0.zip
macOS 10.13 (High Sierra)	SynExtend_1.2.0.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