An interactive application suite/interface for doing Exploration and Significant Biology on a set of Genes.
Note: Above is a screen recoding of SigBio-v0.2.1 (Few thing what you seeing in this recoding might be different when you download a recent version, as this project is going under rapid changes).
Try yourself?
Few note before you start using -
- The application will take a while to start as initially, because it try to fetch and set up the basic database.
- Few componets of this application requires atleast 4 GB of system memory. So It might crash if no sufficient memory availbile.
Do it in your own computer system by following installation instructions or try one of the following methods.
A demo instance - https://sksahu.shinyapps.io/sigbio/ (the above note applies to this as well)
Table Of Content
The main motivation is to provide an easy interface to explore a Gene-set, without worrying about getting an organism database or conversion between particular R object which can be input to an available awesome R/Bioconductor package.
After downstream analysis of gene expression data, the end results are often a set of genes (may be a list of clustered genes, up/down regulated genes). To know their biological significance on a particular context (gene ontology or pathway) lot of statistical analysis available (Gene set enrichment, Over representation). Some awesome Bioconductor packages are developed for this purpose, But often the entry point might be difficult in some cases (mostly because of a particular input type). Also, besides that specifically for non-model organism it is little challenging.
Trying to solve these problems sig-bio-shiny is made. Completely made using R and Bioconductor. No manual database dump required, which make deployment simple with a single R Script. It takes full advantage of AnnotationHub package to get latest annotation for the selected organism and do statistical analysis on top of it using various well known packages.
- Model and Non-model organism support with AnnotationHub
- Internal conversion of R objects for suitable input to a particular package/function/module.
- Modules
- Gene mapping Annotation
- Gene Ontology (GO) Enrichment
- KEGG Pathway Enrichment
- Reproducible code (#25)
- Report generation
- Support for DESeq2 results object as input.
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.
R >= 3.5
From R console
if (!require(remotes)) { install.packages("remotes") }
remotes::install_github("sk-sahu/sig-bio-shiny")Launch the app in browser.
SigBio::runApp()First you need to install the SigBio package which have all the APIs required for most functionality in the shiny app.
Download the app.R file using wget from a specific app directory of your shiny-server.
wget https://raw.githubusercontent.com/sk-sahu/sig-bio-shiny/master/inst/app/app.R -O sig-bio-shiny-app.ROn the first time of running This will download and install all the required dependency.
docker pull sudosk/sig-bio-shiny:latest
docker run --user shiny --rm -p 80:3838 sudosk/sig-bio-shiny:latestAccessed app in a browser at http:https://127.0.0.1
This is an open project. Please feel to contribute.
Here is a guide for start with contributing.
Please note that the SigBio project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.