ClinPOP is a web application to visualize and analyse selected ClinVAR marker frequencies in regional populations over time. The interactive web interface, build in shiny dashboard web application, contains different frequency plots and overviews for the selected input.
Version: 1.0.8
Author: Dominique Fastus
Requires: R (shiny, shinydashboard, dplyr,
tidyverse, openxlsx, ggplot2,
plotly, DT)
Python (argparse) [OPTIONAL]
Run: ClinPOPapp.R for shiny application
ClinPOPsetup.R + REplink.py for data
implementation and setup changes
Website: to be deployed ...
The following datasets were provided and used:
Plink files
- Data_public.bed
- Data_public.bim
- Data_public.fam
To read more over plink and the file formats : https://www.cog-genomics.org/plink/
Ancient dataset with indivdual informations
- Eurasian - Dataset_tims.xlsx
The ClinVAR marker information or variant summary of the NCBI database can be downloaded through the ftp site:
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz
To prepare the data follow the steps in the ClinPOPsetup.R
script.
To run the application open ClinPOPapp.R
in R studio and install necessary packages and open the web application in your browser from the viewer panel.