Shiny Genome Stats

R Shiny app to show basic statistics and features of microbial genomes.

Available on Shinyapps.io!

Features

• shows number of proteins broken down by categories such as 'reviewed', 'hypothetical', etc.
• shows presumed localization of proteins
• shows length/size distribution of proteins
• summarized biological processes: top 20 GO terms by number of proteins annotated for the respective term
• genomic features: currently number, name and length of the different chromosomes/plasmids per strain
• if you like to see more features, please request by posting a github issue

Getting started

Run the app at https://m-jahn.shinyapps.io/shiny-genome-stats/!

If you want to run this app locally, you need to have R > 4.0.0 (optionally also Rstudio) and these libraries installed:

• shiny
• httr
• jsonlite
• DT
• shinyWidgets
• tidyr
• dplyr
• readr
• ggplot2
• shinythemes
• shinyTree
• configr
• stringr
• colorspace
• forcats
• rentrez

Open global.R, server.R or ui.R in RStudio and push the Run App button in Rstudio, done! You can also run the app from R console, just call runApp("path-to-ShinyApp").

Input data

shiny-genome-stats retrieves data dynamically from uniprot.org and NCBI. In order to speed things up, the app comes with currently six microbial proteomes pre-downloaded.

• Cupriavidus necator H16, taxonomy ID 381666
• Bacillus subtilis 168, taxonomy ID 224308
• Salmonella typhimurium LT2, taxonomy ID 99287
• Escherichia coli BL21, taxonomy ID 469008
• Pseudomonas putida KT2440, taxonomy ID 160488
• Streptococcus pyogenes serotype M1 GAS, taxonomy ID 301447

Structure

This app consists of a set of R scripts that determine the functionality.

• global.R loads packages, data sets, and .yml configuration files
• server.R contains the main body of functions. The server obtains input parameters from the GUI and adjusts the graphical output accordingly (changes charts on the fly)
• ui.R The GUI contains the interactive modules such as sliders and check boxes
• R/<helper_functions>.R - additional functions loaded when necessary, for example for data formatting and plotting

Author(s)

• Dr. Michael Jahn
  • Affiliation: Max-Planck-Unit for the Science of Pathogens (MPUSP), Berlin, Germany
  • ORCID profile: https://orcid.org/0000-0002-3913-153X
  • github page: https://github.com/m-jahn