sitePath

DOI: 10.18129/B9.bioc.sitePath    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see sitePath.

Detection of sites with fixation of amino acid substitutions in protein evolution

Bioconductor version: 3.11

The package does hierarchical search for fixation events given multiple sequence alignment and phylogenetic tree. These fixation events can be specific to a phylogenetic lineages or shared by multiple lineages.

Author: Chengyang Ji, Aiping Wu

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	A basic workflow for sitePath
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, MultipleSequenceAlignment, Phylogenetics, SNP, Software
Version	1.4.2
In Bioconductor since	BioC 3.9 (R-3.6) (1.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0)
Imports	ape, seqinr, Rcpp, methods, graphics, utils, stats
LinkingTo	Rcpp
Suggests	testthat, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/wuaipinglab/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_1.4.2.tar.gz
Windows Binary	sitePath_1.4.2.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	sitePath_1.4.2.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