SynExtend

This is the development version of SynExtend; for the stable release version, see SynExtend.

Tools for Working With Synteny Objects

Bioconductor version: Development (3.21)

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] (ORCID: ), Aidan Lakshman [aut, ctb] (ORCID: ), 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 "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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	1.19.0
In Bioconductor since	BioC 3.11 (R-4.0) (4.5 years)
License	GPL-3
Depends	R (>= 4.4.0), 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

Package Archives

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

Source Package	SynExtend_1.19.0.tar.gz
Windows Binary (x86_64)	SynExtend_1.19.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
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