https://github.com/nasqar/deseq2shiny

a web-based R shiny application that wraps DESeq2 R package
https://github.com/nasqar/deseq2shiny

bioinformatics bulk-rna-seq deseq2 r rna-seq rna-seq-analysis rshiny shiny shinyapps visualization webapplication

Last synced: 8 days ago
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a web-based R shiny application that wraps DESeq2 R package

• Host: GitHub
• URL: https://github.com/nasqar/deseq2shiny
• Owner: nasqar
• Created: 2018-10-24T11:55:49.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2020-04-19T12:59:21.000Z (over 4 years ago)
• Last Synced: 2024-08-13T07:14:55.055Z (4 months ago)
• Topics: bioinformatics, bulk-rna-seq, deseq2, r, rna-seq, rna-seq-analysis, rshiny, shiny, shinyapps, visualization, webapplication
• Language: R
• Homepage: http://nasqar.abudhabi.nyu.edu/deseq2shiny/
• Size: 2.27 MB
• Stars: 15
• Watchers: 2
• Forks: 7
• Open Issues: 4
• Metadata Files:
  • Readme: README.md

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• jimsghstars - nasqar/deseq2shiny - a web-based R shiny application that wraps DESeq2 R package (R)

README

        
## DESeq2Shiny: a web-based app based on the DESeq2 R package for RNA-seq counts data exploratory analysis and differential expression

### Introduction

---

This Shiny app is a wrapper around **DESeq2**, an R package for **"Differential gene expression analysis based on the negative binomial distribution".**

It is meant to provide an intuitive interface for researchers to easily **upload, analyze, visualize, and explore RNAseq count data** interactively with no prior programming knowledge in R.

This tool supports **simple or multi-factorial** experimental design. It also allows for exploratory analysis when no replicates are available.

The app also provides svaseq **Surrogate Variable Analysis** for **hidden batch** effect detection. The user can then include Surrogate Variables (SVs) as adjustment factors for downstream analysis (eg. differential expression). For more information on svaseq, go to this link

### Online/Demo:

You can try it online at http://nasqar.abudhabi.nyu.edu/deseq2shiny

### Pre-print:

[NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization](https://doi.org/10.1101/709980)

### Features

---

Various **visualizations** and **output data** are included:

*   **Clustering**

    *   **R-Log**, **Variance Stabilizing Transformation** (VST) output matrices

    *   **PCA plots**, **Heatmaps**

*   **Differential Expression**

    *   Comparison Data (**logFC, p-value, etc, sample vs sample**, etc …)

    *   MA plots

*   **Gene Expression**

    *   Gene **Boxplots**

      

      

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![alt text](screenshotdeseq2.png "Input Data")