sitePath

DOI: 10.18129/B9.bioc.sitePath    

Detection of site fixation in molecular evolution

Bioconductor version: Release (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>

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

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 1.6.1
In Bioconductor since BioC 3.9 (R-3.6) (1.5 years)
License MIT + file LICENSE
Depends R (>= 3.6.0)
Imports methods, graphics, utils, stats, grDevices, ape, seqinr, Rcpp, gridExtra, RColorBrewer, ggplot2, ggrepel, aplot, tidytree, ggtree
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_1.6.1.tar.gz
Windows Binary sitePath_1.6.1.zip
macOS 10.13 (High Sierra) sitePath_1.6.1.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 3.12 Source Archive

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