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ClinPOP

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 ...

Data preprocessing and ClinPOP setup

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.

Run application

To run the application open ClinPOPapp.Rin R studio and install necessary packages and open the web application in your browser from the viewer panel.