SynExtend

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see SynExtend.

Tools for Working With Synteny Objects

Bioconductor version: 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 iD ORCID: 0000-0002-6029-304X , Aidan Lakshman [aut, ctb] ORCID iD 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")):

Installation

To install this package, start R (version "4.5") 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 1.20.2

In Bioconductor since BioC 3.11 (R-4.0) (5.5 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

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Build Report Build Report

Package Archives

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

Source Package SynExtend_1.20.2.tar.gz

Windows Binary (x86_64) SynExtend_1.20.2.zip

macOS Binary (x86_64) SynExtend_1.20.2.tgz

macOS Binary (arm64) SynExtend_1.20.2.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

Old Source Packages for BioC 3.21 Source Archive