class: center, middle, inverse, title-slide # SigBio-Shiny ## A standalone interactive application for detecting biological significance on a GeneSet ### <a href="https://sksahu.net">Sangram Kesahri Sahu</a> ### Bangalore, India ### 2020/07/01 (Updated: 2020-07-05) --- layout: true <div class="my-footer"><span> https://sksahu.net/sigbio-shiny-slides          </span></div> --- # Outlines - What is detecting Biological Significance on a GeneSet means? - Some of available resources - Ideal scenarios for a GeneSet analysis - SigBio-Shiny Overview - Features - Usage - Screenshots/Demo - Modular Design for developers --- # Biological Significance on a GeneSet  --- # Some of available resources  --- # Ideal scenarios for a GeneSet analysis .pull-left[ - An organism database - From **Up-to-date resources** - Support for **model and non-model organisms/species** - Reproducibility - Keeping track of **Database version** - Statistical iterations log - Accessibility - **Programmatic access** alongside GUI - Result interpretability with **plots** ***While most available resources support some of above criteria but not all.*** ] .pull-right[  ] --- # SigBio-Shiny Overview SigBio-Shiny provides a standalone R-Shiny based GUI application for doing such GeneSet based analysis. Build on top of already available **open-source infrastructure**, Such as -  --- # SigBio-Shiny Structure  --- # SigBio-Shiny Features - Run time **downloading of selected organism database** with keeping a log for reproducibility. (with [AnnotationHub]) - **Gene ID mapping** from different database. (with [AnnotationDbi]) - **Gene Ontology Enrichment** (with [clusterProfiler]) - **KEGG pathway Enrichment** (with [clusterProfiler]) - Visualization of **genes in KEGG pathway** (with [pathview]) - Different **enrichment plots** (with [enrichplot]) [AnnotationHub]: https://bioconductor.org/packages/release/bioc/html/AnnotationHub.html [clusterProfiler]: https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html [pathview]: https://bioconductor.org/packages/release/bioc/html/pathview.html [enrichplot]: https://www.bioconductor.org/packages/release/bioc/html/enrichplot.html ## Work in progress - Directly launch with R objects from certain packages like DESeq2 - Complete **reproducible R-script** in the end of an analysis. --- # SigBio-Shiny Usage - Download as **R-package** and launch into browser directly from R console ```r remotes::install_github("sk-sahu/sig-bio-shiny") # Install the package SigBio::runApp() # Load the shiny application in browser SigBio::runApp(res) # work in progress ``` - Download as a **single R-script** for Shiny-Server deploy ```bash wget https://raw.githubusercontent.com/sk-sahu/sig-bio-shiny/master/inst/app/app.R -O sig-bio-shiny-app.R ``` - Also can be run from a readily available **docker container**. ```bash docker pull sudosk/sig-bio-shiny:latest docker run --user shiny --rm -p 80:3838 sudosk/sig-bio-shiny:latest ``` --- # SigBio-Shiny Demo <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;"> <iframe src="https://www.youtube.com/embed/Ij-pPLaXUAc" style="position: absolute; top: 0; left: 0; width: 100%; height: 90%; border:0;" allowfullscreen></iframe> </div> --- # SigBio-Shiny New UI  --- # SigBio-Shiny Modular Design  Build on a modular approach such that adding a new package/functionality is easy for a developers. --- .center[ # Thank you ] Project Github - https://github.com/sk-sahu/sig-bio-shiny/ Open to Feedback or Contributions - [Project's GitHub Issue section](https://github.com/sk-sahu/sig-bio-shiny/issues) - [Project's Gitter chat room](https://gitter.im/sig-bio-shiny/community) - Or directly reach me on twitter [@sangram_ksahu](https://twitter.com/sangram_ksahu) This Side URL: [https://sksahu.net/sigbio-shiny-slide](https://sksahu.net/sigbio-shiny-slides)