How mrugakshi77/pss_scrna_biomarker_discovery works
This repository reproduces a pSS single-cell RNA-seq analysis and presents its results in a Shiny biomarker explorer. The documented workflow runs from GEO data download through quality control, normalization, dimensionality reduction, clustering, and differential expression; a preparation script extracts lightweight app data, which supports interactive visualization. The README documents these stages and app capabilities, but no source excerpts were available, so implementation-level calls and the exact use of individual data files cannot be verified.
Main entry points: pss_workflow.ipynb Single-cell analysis · prepare_app_data.r Data preparation · app_data.rds Prepared app data · App.R Shiny dashboard
Components 5
Analysis pipeline
- Single-cell analysis
pss_workflow.ipynb
App data
- Data preparation
prepare_app_data.r - Prepared app data
app_data.rds
Interactive explorer
- Shiny dashboard
App.R
Other components
- GEO dataset
Connections 4
- GEO dataset → Single-cell analysis: downloads data
README.md - Single-cell analysis → Data preparation: provides analysis results
- Data preparation → Prepared app data: extracts data
README.md - Prepared app data → Shiny dashboard: supplies app data