Skip to content

README.md

Latest commit

 

History

History
29 lines (17 loc) · 937 Bytes

README.md

File metadata and controls

29 lines (17 loc) · 937 Bytes

Gene expression in public RNA-Seq data for adult Zebrafish tissues.

In which tissue my favorite gene is expressed?

I used STAR to map the publicly available RNA-Seq data and Kallisto to quantify expression.

Usage:

Using interactive app:

Go to https://slebedeva.shinyapps.io/zebrafish-tissue-expression/

Deployment script is courtesy of Roel M. Hogervorst (https://www.r-bloggers.com/2021/02/deploy-to-shinyapps-io-from-github-actions/)

If you have Rstudio installed locally:

Open Rstudio and type:

library("shiny")
runGitHub("public_rnaseq_tpm","slebedeva")

Enter your gene as official gene symbol (case-sensitive!) (piwil1) or Ensembl gene name (ENSDARG...). Mouse over the bar to see the sample and the TPM. The plot is showing total expression per gene. You can also download the counts as a table.