sitePath

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see sitePath.

Phylogenetic pathway–dependent recognition of fixed substitutions and parallel mutations


Bioconductor version: 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>

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

Installation

To install this package, start R (version "4.1") and enter:


if (!require("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")
An introduction to sitePath HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, MultipleSequenceAlignment, Phylogenetics, SNP, Software
Version 1.8.4
In Bioconductor since BioC 3.9 (R-3.6) (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
System Requirements
URL https://wuaipinglab.github.io/sitePath/
Bug Reports https://github.com/wuaipinglab/sitePath/issues
See More
Suggests BiocStyle, devtools, knitr, magick, rmarkdown, testthat
Linking To Rcpp
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 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
Bioc Package Browser https://code.bioconductor.org/browse/sitePath/
Package Short Url https://bioconductor.org/packages/sitePath/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive