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README.md
# PhyloProfile [![Bioconductor](https://img.shields.io/badge/available%20at-Bioconductor-orange)](https://bioconductor.org/packages/PhyloProfile) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-phyloprofile/README.html) [![published in: Bioinformatics](https://img.shields.io/badge/published%20in-Bioinformatics-ff69b4.svg?style=flat)](https://doi.org/10.1093/bioinformatics/bty225) [![presented at: GCB2018](https://img.shields.io/badge/presented%20at-GCB2018-green.svg?style=flat)](http://gcb2018.de) [![poster at: SMBE2019](https://img.shields.io/badge/poster%20at-SMBE2019-green)](https://f1000research.com/posters/6-1782) [![BioC status](http://www.bioconductor.org/shields/build/devel/bioc/PhyloProfile.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/PhyloProfile) ![](https://github.com/BIONF/phyloprofile-data/blob/gh-pages/www/posterSub.png) [Click here for the full PDF version of the BOSC2017 poster](https://f1000research.com/posters/6-1782) *PhyloProfile* is an R package that comes together with a *Shiny*-based tool for integrating, visualizing and exploring multi-layered [phylogenetic profiles](https://en.wikipedia.org/wiki/Phylogenetic_profiling). Alongside the presence/absence patterns of [orthologs](https://en.wikipedia.org/wiki/Homology_(biology)) across large [taxon](https://en.wikipedia.org/wiki/Taxon) collections, *PhyloProfile* allows the integration of any two additional information layers. These complementary data, like [sequence similarity](https://en.wikipedia.org/wiki/Sequence_alignment) between orthologs, similarities in their [domain architecture](https://www.ncbi.nlm.nih.gov/pubmed/20221914), or differences in [functional annotations](https://en.wikipedia.org/wiki/Protein_function_prediction) enable a more informed interpretation of phylogenetic profiles. By utilizing the [NCBI taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy), *PhyloProfile* can dynamically collapse taxa into higher [systematic groups](https://en.wikipedia.org/wiki/Taxonomy_(biology)). This enables rapidly changing the resolution from the comparative analyses of proteins in individual species to that of entire kingdoms or even domains without changes to the input data. *PhyloProfile* furthermore allows for a dynamic filtering of profiles – taking the taxonomic distribution and the additional information layers into account. This, along with functions to estimate [the age of genes](http://www.cell.com/trends/genetics/fulltext/S0168-9525(13)00111-X) and [core gene](https://en.wikipedia.org/wiki/Pan-genome) sets facilitates the exploration and analysis of large phylogenetic profiles. Take a look at [the functionality](https://github.com/BIONF/PhyloProfile/wiki/Functionality) of *PhyloProfile* and [explore the installation-free online version](http://applbio.biologie.uni-frankfurt.de/phyloprofile/) to learn more. # Table of Contents * [Installation & Usage](#installation--usage) * [Input Data](#input-data) * [Walkthrough & Examples](#walkthrough--examples) * [Bugs](#bugs) * [Acknowledgements](#acknowledgements) * [License](#license) * [How-To Cite](#how-to-cite) * [Contact](#contact) # Installation & Usage *PhyloProfile* requires the latest version of [R](https://cran.r-project.org) (check for required R version [here](https://bioconductor.org/packages/PhyloProfile)). Please install or update R on your computer before continue. * [R for Linux](https://cran.r-project.org/bin/linux/) * [R for Mac OS](https://cran.r-project.org/bin/macosx/) * [R for Windows](https://cran.r-project.org/bin/windows/base/) Then start R to install and use *PhyloProfile*. ## Using BiocManager *PhyloProfile* is available at [Bioconductor](https://bioconductor.org/packages/PhyloProfile) (require Bioc version ≥ 3.14). To install *PhyloProfile*, start R and enter: ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("PhyloProfile") ``` To install the development version of PhyloProfile, please use the [devel version](https://bioconductor.org/developers/how-to/useDevel/) of Bioconductor: ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version='devel') BiocManager::install("PhyloProfile") ``` or *install the dev version of *PhyloProfile* from our github repository using __[devtools](https://cran.r-project.org/web/packages/devtools/index.html)__.* ## Using devtools The dev version of *PhyloProfile* can be installed from this github repository using `devtools`: ```r if (!requireNamespace("devtools")) install.packages("devtools") devtools::install_github("BIONF/PhyloProfile", INSTALL_opts = c('--no-lock'), build_vignettes = TRUE) ``` ## Using Conda *PhyloProfile* can also be installed within a [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/) environment. First, add [bioconda](https://bioconda.github.io/user/install.html#set-up-channels) to the list of your conda channels: ``` conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge ``` then install *PhyloProfile* using the standard `conda install` command: ``` conda install bioconductor-phyloprofile ``` This installation step can take a while regardless of the method used, as all necessary dependencies will be downloaded and installed automatically. *(Note: Depending on your system this sometimes fails, please check the console log for error messages concerning the dependency installation)* ## Start PhyloProfile's Shiny app From the R terminal, enter: ```r library(PhyloProfile) runPhyloProfile() ``` Check your web browser, *PhyloProfile* will be displayed there ;-) For the first time running, the tool will download a [pre-caculated taxonomy data](https://github.com/BIONF/phyloprofile-data). Please be patient until you see a message for uploading input files. _**Please check our [detailed instructions](https://github.com/BIONF/PhyloProfile/wiki/Installation) if you encounter any problems while installing and starting the program.**_ # Input Data *PhyloProfile* can read a number of different input files, including multi-FASTA files, regular tab-separated files, OMA ID lists or *OrthoXML* files. The additional information layers can be embedded in the OrthoXML or be provided separately as tab-separated files. We described all suppported input formats in section [Input Data](https://github.com/BIONF/PhyloProfile/wiki/Input-Data) in our [PhyloProfile's Wiki](https://github.com/BIONF/PhyloProfile/wiki). # Walkthrough & Examples Read the [walkthrough slides](https://github.com/BIONF/PhyloProfile/wiki/Walkthrough) to explore the functionality of the *PhyloProfile* GUI. Check the vignette for learning how to use PhyloProfile's functions in some specific use-cases: ```r browseVignettes("PhyloProfile") ``` # Bugs Any [bug reports or comments, suggestions](https://github.com/BIONF/PhyloProfile/blob/master/CONTRIBUTING.md) are highly appreciated. Please [open an issue on GitHub](https://github.com/BIONF/PhyloProfile/issues/new) or be in touch via email. # Acknowledgements We would like to thank 1) [Bastian](https://github.com/gedankenstuecke) for the great initial idea and his kind support, 2) Members of [Ebersberger group](http://www.bio.uni-frankfurt.de/43045195/ak-ebersberger) for many valuable suggestions and ...bug reports :) # Contributors * [Vinh](https://github.com/trvinh) * [Bastian](https://github.com/gedankenstuecke) * [Carla](https://github.com/CarlaMoelbert) # License This tool is released under [MIT license](https://github.com/BIONF/PhyloProfile/blob/master/LICENSE). # How-To Cite Ngoc-Vinh Tran, Bastian Greshake Tzovaras, Ingo Ebersberger, PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages 3041–3043, https://doi.org/10.1093/bioinformatics/bty225 or use the citation function in R CMD to have it directly in BibTex or LaTeX format ```r citation("PhyloProfile") ``` # Contact Vinh Tran tran@bio.uni-frankfurt.de