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A standalone R shiny application for doing significant biology on a set of genes
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README.md

sig-bio-shiny

Lifecycle: experimental Build Status CircleCI GitHub release (latest by date) Docker Cloud Build Status

R shiny application for doing significant biology on a set of genes.

Demo

Introduction

Significant Biology is an important step of any high-throughput sequence analysis. Once you mapped and/or assembled sequenced reads followed by feature(gene/isoform) quantification and/or diffrential analysis you will end up with set of genes. Quickly exploring those genes from diffrent aspect what gives an idea about the Biology they involved in. Here comes this SigBio Shiny application. This is platform where with a set of genes you can do Gene Ontology (GO), KEGG Pathway, Enrichment, Annotation and many things (will be discussed soon).

This is completely writen in R Shiny (if the name not already referes) and underneeth uses R and Bioconductor packages.

Disclaimer

sig-bio-shiny shiny application along with the SigBio R package is an open source effort and distributed under MIT license. This uses KEGG data for few tasks, which is free for Academic uses but other uses may require a license agreement (In details at KEGG Website). By using this application you follow the respective tool licenses. Any developer involved in this DO NOT warrant nor responsible for any legal issues.

Requirements

R >= 3.5

Download

First you need to install the SigBio package which have the APIs required for most functionality in the app.

if (!require(remotes)) { install.packages("remotes") }
  remotes::install_github("sk-sahu/sig-bio-shiny", 
                          ref = "v0.2.1")

Download a specific version of the app using wget from terminal

wget https://raw.githubusercontent.com/sk-sahu/sig-bio-shiny/v0.2.1/app.R -O sig-bio-shiny-app-v0.2.1.R

On the first time of running This will download and install all the required dependency.

Run the shiny app

From your terminal

Rscript sig-bio-shiny-app-v0.2.1.R

Access the app in your browser with output URL.

Run with docker

docker pull sudosk/sig-bio-shiny:v0.2.1
docker run --user shiny --rm -p 80:3838 sudosk/sig-bio-shiny:v0.2.1

Accessed app in a browser at http://127.0.0.1

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