README.md

In aariani/easyLG: A shiny app for landscape genomic analysis

easyLG: Landscape genomics made easy!

This R package launch a shiny app for landscape genomic analysis. The Shiny app was developed in the LGapp repo. We included the code in an R packages for ease of use

Overview

The package consists of 3 functions:

1. easyLG_app(): is the main function launching the shiny app.

2. easyLG_check(): check the presence of all the dependencies needed by the package. If the dependencies are not present in your system they will be installed.

3. easyLG_update() : install all the dependencies needed. Could be used for updating the dependencies.

Before starting

Please follow the order of the different subheaders for dependencies installation

Ubuntu libraries

For installing and running the package in Ubuntu you will need to install several libraries like the RcppEigen, libcurl and libssl.

From the terminal type:

    sudo apt-get install r-cran-rcppeigen
    sudo apt-get install libcurl4-openssl-dev libssl-dev

Windows

For Windows you will need to install the curl library in R.

From within R type:

install.packages('curl')

Install R devtools

The package requires the installation of the devtools R package before starting.

For informations about installing devtools on different system please visit the devtools website or the README file.

Download bioclimatic data

You will need to download bioclimatic data (BIO1-BIO19) from the Worldclim database into your system.

For windows users please save the bioclim data into your C:\User\YOURNAME\Documents\ folder

Installation

For install the easyLG package in your system open R or RStudio and type in the terminal:

library(devtools)
install_github('aariani/easyLG')

Before starting the easyLG_app() please check if all the package dependencies are installed by opening R or RStudion and type in the terminal:

easyLG_check()

This step will check if the dependencies are installed. If not the function will install them directly in your system.

Tutorials and example dataset

For a more detailed tutorial please visit the wiki page of this repo.

For an exaple dataset please downloads the SNPs file (in VCF format) and the coordinates file here

aariani/easyLG documentation built on Sept. 27, 2019, 4:22 p.m.