sitePath
Phylogeny-based sequence clustering with site polymorphism
Bioconductor version: Release (3.20)
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("sitePath")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, MultipleSequenceAlignment, Phylogenetics, SNP, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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_1.22.0.tar.gz |
| Windows Binary (x86_64) | sitePath_1.22.0.zip |
| macOS Binary (x86_64) | sitePath_1.22.0.tgz |
| macOS Binary (arm64) | sitePath_1.22.0.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 |