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sitePath

This is the development version of sitePath; for the stable release version, see sitePath.

Phylogeny-based sequence clustering with site polymorphism


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

Details

biocViews Alignment, MultipleSequenceAlignment, Phylogenetics, SNP, Software
Version 1.19.0
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_1.19.0.tar.gz
Windows Binary sitePath_1.19.0.zip
macOS Binary (x86_64) sitePath_1.19.0.tgz
macOS Binary (arm64) sitePath_1.19.0.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