This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see sitePath.
Bioconductor version: 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")
):
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.
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 |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | Alignment, MultipleSequenceAlignment, Phylogenetics, SNP, Software |
Version | 1.6.6 |
In Bioconductor since | BioC 3.9 (R-3.6) (2 years) |
License | MIT + file LICENSE |
Depends | R (>= 4.0.0) |
Imports | RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils |
LinkingTo | Rcpp |
Suggests | BiocStyle, knitr, 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 |
Follow Installation instructions to use this package in your R session.
Source Package | sitePath_1.6.6.tar.gz |
Windows Binary | sitePath_1.6.6.zip (32- & 64-bit) |
macOS 10.13 (High Sierra) | sitePath_1.6.6.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 |
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