https://github.com/datasnakes/rnaseek
A shiny app to perform single and multifactor differential analysis using DESeq2, edgeR, and limma
https://github.com/datasnakes/rnaseek
count-table deseq2 htseq r rna-seq rnaseq shiny shiny-apps
Last synced: 7 months ago
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A shiny app to perform single and multifactor differential analysis using DESeq2, edgeR, and limma
- Host: GitHub
- URL: https://github.com/datasnakes/rnaseek
- Owner: datasnakes
- Created: 2017-06-15T16:40:38.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2018-12-08T03:19:57.000Z (almost 7 years ago)
- Last Synced: 2025-01-17T03:46:23.393Z (9 months ago)
- Topics: count-table, deseq2, htseq, r, rna-seq, rnaseq, shiny, shiny-apps
- Language: HTML
- Homepage: http://www.datasnakes.org/RNASeek
- Size: 48.7 MB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
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README
# 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`](https://github.com/datasnakes/htseq-count-cluster) merged counts table or merge counts table from [htseq](https://github.com/simon-anders/htseq)'s `htseq-count` script and a matching annotation table or csv file.
## Running the RNASeek app locally
### Via the runGitHub command
```r
library(shiny)
shiny::runGitHub('RNASeek', 'datasnakes')
```
### Via cloning the repository
1. Clone or download the git repository.
```bash
git clone https://github.com/datasnakes/RNASeek.git
```
2. Open RStudio or Rconsole and type:
```r
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
```r
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
```
## Maintainers
Shaurita Hutchins | [@sdhutchins](https://github.com/sdhutchins) | [✉](mailto:sdhutchins@outlook.com)
Rob Gilmore | [@grabear](https://github.com/grabear) | [✉](mailto:robgilmore127@gmail.com)
Please feel free to [open an issue](https://github.com/datasnakes/RNASeek/issues/new) if you have a question, feedback, or problem using this app.