Radish is a shiny application for the visualisation and analysis of pre-processed RNA-seq data, specifically differential expression analysis. Given data processed with GENOM'IC's pipeline, it is able to produce customisable plots, such as PCA plots, Volcano plots and Heatmaps. It also allows one to explore the counts and results table interactively.
Radish is an exploration tool, it relies on data already processed from raw reads, following a STAR -> RSEM -> DESeq2 pipeline, with gene name annotation with Biomart.
Installation is only available through docker for now.
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First, install Docker : https://docs.docker.com/get-docker/
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Then run (on Windows, use the command prompt):
docker pull bsgenomique/radish docker run -dp 80:3838 --rm bsgenomique/radish -
Access the app through your usual web navigator (Chromium-based, there is an issue with Firefox and the tutorial videos), at the adress http://localhost/.
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Load your
result.rdsfile in the Data tab -
Explore!
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Don't forget to stop the container afterwards!
Follow the instructions in the app. Load the results.rds file provided by GENOM'IC in the Data tab, and then proceed to explore the dataset and produce your figures!
To experiment with the app, you can use demo data kindly provided by Juliette Paillet (Kroemer team, UMRS1138), from this article by Paillet et al. (raw data otherwise available from Gene Expression Omnibus, under accession no. GSE180289). It is accessible by a simple button press!
If you have any comment, suggestion or question, feel free to post an issue.
Main contributors to this project are Paul Etheimer (Developpement, documentation, testing) under the supervision of Juliette Hamroune (Initiator, evaluation, feature suggestions).