PhyloProfile
This is the development version of PhyloProfile; for the stable release version, see PhyloProfile.
PhyloProfile
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Vinh Tran <tran at bio.uni-frankfurt.de>
citation("PhyloProfile")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataRepresentation, DimensionReduction, FunctionalPrediction, MultipleComparison, Software, Visualization |
| Version | 1.99.1 |
| In Bioconductor since | BioC 3.10 (R-3.6) (5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, dplyr, DT, energy, ExperimentHub, extrafont, fastcluster, ggplot2, gridExtra, pbapply, plotly, RColorBrewer, RCurl, Rfast, scattermore, shiny, shinyBS, shinycssloaders, shinyFiles, shinyjs, stringr, tsne, umap, 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 | |
| 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 | PhyloProfile_1.99.1.tar.gz |
| Windows Binary (x86_64) | PhyloProfile_1.99.1.zip |
| macOS Binary (x86_64) | PhyloProfile_1.99.1.tgz |
| macOS Binary (arm64) | PhyloProfile_1.99.1.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 |