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:
Maintainer: Nicholas Cooley <npc19 at pitt.edu>
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 | ||
| NEWS | Text |
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/ |
See More
| 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 (64-bit only) |
| macOS Binary (x86_64) | SynExtend_1.19.0.tgz |
| macOS Binary (arm64) | SynExtend_1.19.0.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 |