Differential Expression Analysis [Protein/Gene/...] deployed via GH actions to shinyapp.io

app: Shiny/R application for differential-expression analysis using T-test based on VolcaNoseR

fix: Automatically deployed via GH Actions to shinyapp.io available as https://fuzzylife.shinyapps.io/diffExpr/ using heroku deployment strategy of https://blog.simonpcouch.com/blog/r-github-actions-commit/

source: https://github.com/animesh/r-source/blob/master/src/library/stats/R/t.test.R mailto: sharma.animesh@gmail.com?subject=diffExprApp

git clone https://github.com/animesh/diffExpr
usethis::create_package(path = "diffExpr")

tested with proteinGroups.txt from Proteomics profiling in primary tumors of metastatic and non-metastatic breast cancers results

wget https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/03/PXD037288/txt.zip
unzip txt.zip

where T67 is Groups 1 is representing samples 43_|44_|45_|46_|47_|48_ (note that individual samples at separated by pipe) and samples representing Group 2/T66 are is 37_|38_|39_|40_|41_|42_, the results downloaded for this comparison in above zip file proteinGroups.txtLFQ.intensity.112T67T660.050.50.05tTestBH.csv should match with the ones Downloaded from this analysis

base:

deps

library(curl) library(jsonlite)

run

cron: "0 * * * *"

o Install

Server

sudo su - -c "R -e \"install.packages(c('ggplot2','dplyr','ggrepel','shinycssloaders','readxl','DT', 'RCurl','svglite')repos='https://cran.rstudio.com/')\""

o log monitor example

tail -f /var/log/shiny-server/VolcaNoseR-shiny-*.log

o The first option is running it directly from Github. In the command line (in R or Rstudio) type:

shiny::runGitHub('VolcaNoseR', 'animesh')
o The second option is download the app and to use it offline:

-download the app.R and csv files (Data-Vulcano-plot.csv and elife-45916-Cdc42QL_data.csv) with example data.

-Run RStudio and load app.R

-Select 'Run All' (shortcut is command-option-R on a Mac) or click on "Run App" (upper right button on the window)

This should launch a web browser with the Shiny app.

Credits

There are several Shiny apps for Volcano plots that have served as a source of inspiration:

-VolcanoR

-Volcanoshiny

-VolcanoPlot_shiny_app

VolcaNoseR is created and maintained by Joachim Goedhart (@joachimgoedhart)

Example output

Standard output generated with the example data:

Output with user selected annotation of data: