Differential Expression Analysis App (Shiny)

This is a Shiny/R application for differential-expression analysis using T-test followed by Benjamini Hochberg correction (FDR). The app is designed with base-R for proteomics data (MaxLFQ output) and supports quick group-wise comparison with FDR, CV, histograms, heatmap (missing-values as white) and further text-box based search result exploration.

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Features

• Upload or use a default proteinGroups.txt file (tab-separated, MaxLFQ output)
• Dynamically select columns for two groups using prefix and filter patterns
• Default group filters for quick start (e.g., 43_|44_|45_|46_|47_|48_ and 37_|38_|39_|40_|41_|42_)
• Interactive selection of columns for each group
• Real-time display of available columns and sample data
• Row-wise t-test (via custom testT function) between selected groups
• Download results with filename encoding all selection/filter parameters
• Downloaded filename format: proteinGroups_SEL-<selection>_G1-<group1filter>_G2-<group2filter>_testT.csv (all non-alphanumeric characters removed from selection/filter strings)
• Histogram and heatmap of selected data

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Step-by-Step Usage

Figures Generated

• Histogram: Distribution of the selected result column.
• Heatmap of Available Values: Greyscale heatmap (black = available, white = missing/zero) of all selected columns (both groups), transposed for clarity. This helps you quickly assess which proteins/samples have complete or missing data.
• Volcano Plot:
  • X-axis: Log2 median change between groups.
  • Y-axis: -log10(p-value) from the t-test.
  • Points: Black-to-white grayscale by corrected p-value (BH); NA values are white.
  • Vertical lines at x = -1 and x = 1, and a horizontal line at y = -log10(0.05), are drawn for reference.

Setup

Clone the repository

git clone https://github.com/animesh/diffExpr
cd diffExpr
Rscript -e "shiny::runApp('app.R')"
Loading required package: shiny
Warning in warn_if_app_dir_is_package(appDir) :
  Loading R/ subdirectory for Shiny application, but this directory appears to contain an R package. Sourcing files in R/ may cause unexpected behavior. See `?loadSupport` for more details.
Listening on http://127.0.0.1:6266

Install dependencies

install.packages('shiny')

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, proteinGroups_SEL-LFQ_intensity_G1-43_44_45_46_47_48_G2-37_38_39_40_41_42_testT.csv

Credits

There are several Shiny apps for such that have served as a source of inspiration, like:

-VolcanoR

-Volcanoshiny

-VolcanoPlot_shiny_app

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

shiny app running online

Standard output generated with the example data (screenshot):

Note: The heatmap now displays available (non-missing, nonzero) values as black and missing/zero values as white. This is the reverse of the previous logic. The plot is titled "Heatmap of Available Values" and provides a quick visual summary of data completeness across all selected columns.