PhyloProfile

DOI: 10.18129/B9.bioc.PhyloProfile    

PhyloProfile

Bioconductor version: Release (3.10)

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 "3.6") and enter:

if (!requireNamespace("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 1.0.1
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License MIT + file LICENSE
Depends R (>= 3.6.0)
Imports ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, DT, energy, ExperimentHub, ggplot2, grDevices, grid, gridExtra, pbapply, RColorBrewer, shiny, shinyBS, shinycssloaders, shinyjs, stats, utils, OmaDB, plyr, xml2, zoo
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_1.0.1.tar.gz
Windows Binary PhyloProfile_1.0.1.zip
Mac OS X 10.11 (El Capitan) PhyloProfile_1.0.1.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
Old Source Packages for BioC 3.10 Source Archive

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