datasnakes/rnaseek

A shiny app to perform single and multifactor differential analysis using DESeq2, edgeR, and limma

RNASeek

A shiny app to perform single and multifactor differential analyses using edgeR, DESeq2, or limma and create interactive visuzalizations. This app uses the output of a htseq-count-cluster merged counts table or merge counts table from htseq's htseq-count script and a matching annotation table or csv file.

Running the RNASeek app locally

Via the runGitHub command

library(shiny)
shiny::runGitHub('RNASeek', 'datasnakes')

Via cloning the repository

1. Clone or download the git repository.

git clone https://github.com/datasnakes/RNASeek.git

2. Open RStudio or Rconsole and type:

library(shiny)
runApp('path/to/RNASeek')

Dependencies

The dependencies are shiny, shinythemes, and DESeq2. Ensure you have the latest versions installed and the latest version of R.

Update to the latest version of DESeq2

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

Maintainers

Shaurita Hutchins | @sdhutchins | ✉

Rob Gilmore | @grabear | ✉

Please feel free to open an issue if you have a question, feedback, or problem using this app.

rnaseek's Issues

Add interactive plots

Add .travis.yml or continuous integration

Add example dataset

Improve README