SynExtend

This is the development version of SynExtend; for the stable release 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: Development (3.24)

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 1.25.4, 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")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	1.25.4
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, rtracklayer
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_1.25.4.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	SynExtend_1.25.4.tgz
macOS Binary (sonoma-arm64)	SynExtend_1.25.4.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