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Welcome to omicplotR!

omicplotR is an R package that generates a user interface using Shiny to facilitate visual exploration of high-throughput sequencing data without intimate knowledge of the R command line.

Getting started

1. Make sure you have the most recent version of R or RStudio installed. When installing the release branch through Bioconductor, you must have the R version 3.5 or higher.

For Windows:

• Download the setup file for R from the following link: R for Windows
• Open the downloaded .exe file and install R

For Mac:

• Download the appropriate version of .pkg file from the following link: R for Mac

Optionally, you can install RStudio, which gives an interface to use R. I recommended this for new users to R. Download from this link: Download RStudio

Installing Bioconductor release of omicplotR

Install the BiocManager package from CRAN.

install.packages("BiocManager")

Install omicplotR from Bioconductor.

BiocManager::install("omicplotR")

Launch omicplotR in your default browser.

library(omicplotR)
omicplotr.run()

Resizing the window

omicplotR scale relative to the current sizing parameters of your browser. If the font or plots appear too large or small, they can be scaled by zooming in or out using your browser. On macOS, the command is command + and command - for zooming in and out, respectively, while on Windows the command are ctrl + and ctrl -.

Installing the development version

This version will be the most up to date with the newest features. If you want to install the dev version via Bioconductor, you will need to install the R development version (if installing mid-April to mid-October). Instructions can be found here.

install.packages("BiocManager")
BiocManager::install("omicplotR", version = "devel")

Alternatively, you can install directly from this Github page (probably easier).

install.packages("shiny")  
BiocManager::install("ALDEx2")  
install.packages("shiny")  
install.packages("compositions")  
install.packages("zCompositions")  
install.packages("markdown")  
install.packages("propr")   
install.packages("igraph")  
install.packages("devtools")  

Last step. The master branch is the same as Bioconductor development branch. devtools::install_github("dgiguer/omicplotR", ref = "master")

library(omicplotR)
omicplotr.run()