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SynExtend

Tools for Working With Synteny Objects


Bioconductor version: Release (3.18)

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 "4.3") 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")
UsingSynExtend HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, ComparativeGenomics, DataImport, Genetics, Software
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-3
Depends R (>= 4.3.0), DECIPHER(>= 2.28.0)
Imports methods, Biostrings, S4Vectors, IRanges, utils, stats, parallel, graphics, grDevices
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Suggests BiocStyle, knitr, igraph, markdown, rmarkdown
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Package Archives

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

Source Package SynExtend_1.14.0.tar.gz
Windows Binary SynExtend_1.14.0.zip
macOS Binary (x86_64) SynExtend_1.14.0.tgz
macOS Binary (arm64) SynExtend_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SynExtend
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SynExtend
Bioc Package Browser https://code.bioconductor.org/browse/SynExtend/
Package Short Url https://bioconductor.org/packages/SynExtend/
Package Downloads Report Download Stats