PhyloProfile

DOI: 10.18129/B9.bioc.PhyloProfile    

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

PhyloProfile

Bioconductor version: 3.15

PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.

Author: Vinh Tran [aut, cre], Bastian Greshake Tzovaras [aut], Ingo Ebersberger [aut], Carla Mölbert [ctb]

Maintainer: Vinh Tran <tran at bio.uni-frankfurt.de>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PhyloProfile")

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("PhyloProfile")

 

HTML	R Script	PhyloProfile
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataRepresentation, FunctionalPrediction, MultipleComparison, Software, Visualization
Version	1.10.5
In Bioconductor since	BioC 3.10 (R-3.6) (3 years)
License	MIT + file LICENSE
Depends	R (>= 4.2.0)
Imports	ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply, RColorBrewer, RCurl, shiny, shinyBS, shinyFiles, shinyjs, OmaDB, plyr, xml2, zoo, yaml
LinkingTo
Suggests	knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/BIONF/PhyloProfile/
BugReports	https://github.com/BIONF/PhyloProfile/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	PhyloProfile_1.10.5.tar.gz
Windows Binary	PhyloProfile_1.10.5.zip
macOS Binary (x86_64)	PhyloProfile_1.10.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PhyloProfile
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PhyloProfile
Package Short Url	https://bioconductor.org/packages/PhyloProfile/
Package Downloads Report	Download Stats