sitePath

DOI: 10.18129/B9.bioc.sitePath    

This is the development version of sitePath; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.10)

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>

Citation (from within R, enter citation("sitePath")):

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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, Software
Version 1.1.10
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
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://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_1.1.10.tar.gz
Windows Binary sitePath_1.1.10.zip
Mac OS X 10.11 (El Capitan) sitePath_1.1.10.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

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