PhyloProfile
PhyloProfile
Bioconductor version: 3.23 · Package version: 2.4.7
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PhyloProfile")Details
| Maintainer | Vinh Tran <v.tran@ub.uni-frankfurt.de> |
| Author | Vinh Tran [aut, cre] (ORCID: <https://orcid.org/0000-0001-6772-7595>), Bastian Greshake Tzovaras [aut], Ingo Ebersberger [aut], Carla Mölbert [ctb] |
| License | MIT + file LICENSE |
| URL | https://github.com/BIONF/PhyloProfile/ |
| Bug Reports | https://github.com/BIONF/PhyloProfile/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataRepresentation, DimensionReduction, FunctionalPrediction, MultipleComparison, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/PhyloProfile/ |
Citation
From within R, enter citation("PhyloProfile"):
Vinh Tran, Bastian Greshake Tzovaras, Ingo Ebersberger. PhyloProfile: PhyloProfile. doi:10.18129/B9.bioc.PhyloProfile, R package version 2.4.7, https://bioconductor.org/packages/PhyloProfile.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | PhyloProfile_2.4.7.tar.gz |
| Windows binary (x86_64) | PhyloProfile_2.4.7.zip |
| macOS binary (arm64) | PhyloProfile_2.4.7.tgz |
| macOS binary (x86_64) | PhyloProfile_2.4.7.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: ape, bioDist, BiocStyle, Biostrings, bit64, bsplus, colourpicker, data.table, dplyr, DT, energy, fastcluster, ggplot2, gridExtra, htmlwidgets, pbapply, plotly, RColorBrewer, RCurl, scattermore, shiny, shinycssloaders, shinyFiles, shinyjs, stringr, tsne, svglite, umap, xml2, zoo, yaml