Saturation mutagenesis MPRA data access portal

Shiny webapp of https://mpra.gs.washington.edu/satMutMPRA or https://kircherlab.bihealth.org/satMutMPRA/.

Installation

Option 1: conda

If not already done install miniconda

set up the channels:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Then run conda install mpra-data-access-portal

The latest version on conda is 0.1.9 so you can run conda install mpra-data-access-portal=0.1.9 to install exactly this version.

now you can run the data portal via the command: mpra-data-access-portal

The default port is 8080 and the default host 0.0.0.0. If you want to change this please change the two variables SHINY_PORT and export SHINY_HOST. E.g.:

export SHINY_PORT=7001
export SHINY_HOST=127.0.0.1

Then run mpra-data-access-portal again.

Option 2: from source

install dependencies:

R version 4.3.3

R packages:

• dplyr version 1.1.4
• DT version 0.33
• ggplot2 version 3.5.1
• shiny version 1.9.1
• shinytest2 version 0.3.1
• shinyvalidate 0.1.3
• htmlwidgets version 1.6.4
• readr version 2.1.5
• stringr version 1.5.1
• plotly version 4.10.4

You can install also via mamba/conda using: mamba env create -f environment.yaml -n mpra-data-access-portal

Get the latest version via version release on github: https://github.com/kircherlab/MPRA_SaturationMutagenesis/archive/v0.1.9.tar.gz or cloning the repository: https://github.com/kircherlab/MPRA_SaturationMutagenesis/archive/v0.1.9.tar.gz and change to the version tag v0.1.9.

the goto the directory and run the shiny server (here on port 8080 and on host 0.0.0.0, if not alredy defined:

export SHINY_HOST=${SHINY_HOST-0.0.0.0}
export SHINY_PORT=${SHINY_PORT-8080}

Rscript -e "shiny::runApp(port = ${SHINY_PORT}, launch.browser = FALSE, host = '${SHINY_HOST}')"