SynExtend

This is the released version of SynExtend; for the devel version, see SynExtend.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

Tools for Comparative Genomics

Bioconductor version: Release (3.23)

A multitude of tools for comparative genomics, focused on large-scale analyses of biological data. SynExtend includes tools for working with syntenic data, clustering massive network structures, and estimating functional relationships among genes.

Author: Nicholas Cooley [aut, cre] ORCID: 0000-0002-6029-304X , Aidan Lakshman [aut, ctb] ORCID: 0000-0002-9465-6785 , Adelle Fernando [ctb], Erik Wright [aut]

Maintainer: Nicholas Cooley <npc19 at pitt.edu>

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

Nicholas Cooley, Aidan Lakshman, Erik Wright. SynExtend: Tools for Comparative Genomics. doi:10.18129/B9.bioc.SynExtend, R package version 1.24.0, https://bioconductor.org/packages/SynExtend.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, ComparativeGenomics, DataImport, Genetics, Software
Version	1.24.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
License	GPL-3
Depends	R (>= 4.5.0), DECIPHER (>= 2.28.0)
Imports	methods, Biostrings, S4Vectors, IRanges, utils, stats, parallel, graphics, grDevices, RSQLite, DBI
System Requirements
URL	https://github.com/npcooley/SynExtend
Bug Reports	https://github.com/npcooley/SynExtend/issues/new/

Suggests	BiocStyle, knitr, igraph, markdown, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	SynExtend_1.24.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	SynExtend_1.24.0.tgz
macOS Binary (sonoma-arm64)	SynExtend_1.24.0.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