Documentation

GenomicShiny-Cov was tested in windows 10 and Debian/Ubuntu distros, you must be installed R v.4.0 or higher, is not necessary to install Rstudio to run GenomicShiny-Cov.

System requirements

Ubuntu 20.04 / 21.10 / 22.04
Debian 10

Install dependencies for linux ditros

Install dependencies by aptitude:
libprotobuf-dev
libjq-dev
protobuf-compiler
libudunits2-dev
libgdal-dev

Instalation

To run locally the application must be installed first shiny package:

### shiny installation 
install.packages("shiny")

Runing from Github

Copy the following link to install and run GenomicShiny-Cov:

### Copy the link and run in R console  
shiny::runGitHub("GenomicShiny-Cov","FranciscoAscue", 
                    launch.browser = TRUE)

Clone the repository

Linux To run locally clone the repository:

git clone https://github.com/FranciscoAscue/GenomicShiny-Cov.git

cd GenomicShiny-Cov

Rscript app.R

Windows

Download the code from the following LINK and unzipped Open the project in R console :

runApp(launch.browser = TRUE) 

Build docker image

git clone https://github.com/FranciscoAscue/GenomicShiny-Cov.git

cd GenomicShiny-Cov

docker build .

Pull docker images from DockerHub

docker pull fascue/genomicshiny0.1

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Input Files and Usage

File	Description	i.e. Peru	i.e. USA	i.e brazil	i.e. Colombia
Geojson map	Vectorial map	GeoJSON	GeoJSON	GeoJSON	GeoJSON
Metadata from GISAID	Pacient status metadata from EpiCoV GISAID	peru.tsv	usa.tsv	brazil.tsv	colombia.tsv
Epidemiology data	Positive or death cases reported	epiPeru.csv	epiUsa.tsv	epiBrazil.csv	epiColombia.csv