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deseq2shiny's Introduction

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

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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deseq2shiny's People

Contributors

aymanm avatar nasqar avatar

Stargazers

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Watchers

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Forkers

bimberlabinternal sqianglan indianhedgehog yixf-self fentouxungui bassanio

deseq2shiny's Issues

upload of files never done

Hi,
The input file keeps uploading without any further step in the app.
How to circumvent this? It shows no error either.
Kindly help.

DESeq2 Error

Hi,

I performed DGE analysis using example datasets ([dataset] 2016) according to the instructions of Supplementary Materials of your BMC Bioinfo paper.
However, at the step of "Run DESeq2", I got the following error message and could not complete the analysis:
"DESeq2 Error: attempt to select less than one element in OneIndex"

How to circumvent this?

DESeq2 outputs "************" values

Hello,

First, great work on this app. I ran two different data sets (one mouse, one bacterial) and in both cases the DE analysis outputs some values for some genes as " ****************". For example a log2foldchange value for one gene might be that long string of asterisks while all other values for the gene are expected number values. Then a different gene may have an adj p value of '****************e-08' or while other values outputted for that gene are reasonable expected values. I tried to look this up in the DESeq2 manual to see if it is meaningful but it doesn't seem like this is standard output? These data are also not viewable within the shiny app and must be downloaded as .csv. I also tried viewing the .csv vs through the head command in linux to be sure it was a text viewer issue.

Any thoughts on preventing this or a way to see the actual value of these numbers? Thanks!

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