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PhyloProfile

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

PhyloProfile


Bioconductor version: Development (3.20)

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>

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

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("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")
PhyloProfile HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataRepresentation, FunctionalPrediction, MultipleComparison, Software, Visualization
Version 1.19.2
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License MIT + file LICENSE
Depends R (>= 4.4.0)
Imports ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, dplyr, DT, energy, ExperimentHub, extrafont, ggplot2, gridExtra, pbapply, RColorBrewer, RCurl, shiny, shinyBS, shinycssloaders, shinyFiles, shinyjs, stringr, xml2, zoo, yaml
System Requirements
URL https://github.com/BIONF/PhyloProfile/
Bug Reports https://github.com/BIONF/PhyloProfile/issues
See More
Suggests knitr, rmarkdown, testthat, OmaDB
Linking To
Enhances
Depends On Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package PhyloProfile_1.19.2.tar.gz
Windows Binary PhyloProfile_1.19.2.zip
macOS Binary (x86_64) PhyloProfile_1.19.2.tgz
macOS Binary (arm64) PhyloProfile_1.19.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/PhyloProfile
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PhyloProfile
Bioc Package Browser https://code.bioconductor.org/browse/PhyloProfile/
Package Short Url https://bioconductor.org/packages/PhyloProfile/
Package Downloads Report Download Stats