sitePath

DOI: 10.18129/B9.bioc.sitePath    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see sitePath.

Detection of site fixation in molecular evolution

Bioconductor version: 3.12

The package does hierarchical search for fixation mutations given multiple sequence alignment and phylogenetic tree. These fixation mutations can be specific to a phylogenetic lineages or shared by multiple lineages. The package also provides visualization of these mutations on the tree.

Author: Chengyang Ji [aut, cre, cph] , Aiping Wu [ths]

Maintainer: Chengyang Ji <chengyang.ji12 at alumni.xjtlu.edu.cn>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("sitePath")

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("sitePath")

 

HTML	R Script	An introduction to sitePath
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, MultipleSequenceAlignment, Phylogenetics, SNP, Software
Version	1.6.6
In Bioconductor since	BioC 3.9 (R-3.6) (2 years)
License	MIT + file LICENSE
Depends	R (>= 4.0.0)
Imports	RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://wuaipinglab.github.io/sitePath/
BugReports	https://github.com/wuaipinglab/sitePath/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	sitePath_1.6.6.tar.gz
Windows Binary	sitePath_1.6.6.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	sitePath_1.6.6.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sitePath
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/sitePath
Package Short Url	https://bioconductor.org/packages/sitePath/
Package Downloads Report	Download Stats