sitePath

DOI: 10.18129/B9.bioc.sitePath    

Phylogenetic pathway–dependent recognition of fixed substitutions and parallel mutations

Bioconductor version: Release (3.13)

The package does hierarchical search for fixation and parallel mutations given multiple sequence alignment and phylogenetic tree. The package also provides visualization of these mutations on the tree.

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

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

Installation

To install this package, start R (version "4.1") 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	1.8.4
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.1)
Imports	RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils
LinkingTo	Rcpp
Suggests	BiocStyle, devtools, knitr, magick, 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_1.8.4.tar.gz
Windows Binary	sitePath_1.8.4.zip
macOS 10.13 (High Sierra)	sitePath_1.8.4.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
Old Source Packages for BioC 3.13	Source Archive