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>

Citation (from within R, enter citation("SynExtend")):

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: