sitePath

DOI: 10.18129/B9.bioc.sitePath    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see sitePath.

Phylogeny-based sequence clustering with site polymorphism

Bioconductor version: 3.15

Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.

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 "4.2") 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")

 

HTML	R Script	An introduction to sitePath
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, MultipleSequenceAlignment, Phylogenetics, SNP, Software
Version	1.12.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 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_1.12.0.tar.gz
Windows Binary	sitePath_1.12.0.zip
macOS Binary (x86_64)	sitePath_1.12.0.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