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("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 | ||
| 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 |