How chykoushik/tnbc-pdcd1-cd2-scrna-pipeline works
This repository packages a notebook-driven TNBC single-cell RNA-seq analysis and a browser dashboard. The documented workflow starts with GSE176078 data, constructs and validates a cell atlas, stratifies T-cell states, validates patient-level findings against TCGA-BRCA, and ranks engineering targets with stability analysis. The README documents the notebook stages and dashboard contents, but no notebook source excerpts are available, so internal calls and dashboard data wiring cannot be verified; the archive paths identify the documented notebook bundles.
Main entry points: GSE176078_revised.zip Patient aggregation · tnbc_dashboard.html Results dashboard
Components 16
Atlas analysis
- Revised notebook
GSE176078_revised.zip - QC and atlas
GSE176078_revised.zip - Clustering and annotation
GSE176078_revised.zip - T-cell extraction
GSE176078_revised.zip - Module scoring
GSE176078_revised.zip - CD8 stratification
GSE176078_revised.zip
Validation
- Patient aggregation
GSE176078_revised.zip - Survival validation
GSE176078_revised.zip - Ligand-receptor screen
GSE176078_revised.zip
Recommendations
- Priority scoring
GSE176078_revised.zip - Bootstrap stability
GSE176078_revised.zip - Analysis results
GSE176078_revised.zip - Results dashboard
tnbc_dashboard.html
Other components
- Analyst
- NCBI GEO
- UCSC Xena
Connections 18
- Analyst → Revised notebook: runs notebook
- NCBI GEO → Revised notebook: supplies counts
- UCSC Xena → Revised notebook: supplies TCGA data
- Revised notebook → QC and atlas: runs
- QC and atlas → Clustering and annotation: prepares atlas
- Clustering and annotation → T-cell extraction: extracts cells
- T-cell extraction → Module scoring: scores states
- Module scoring → CD8 stratification: stratifies
- CD8 stratification → Patient aggregation: aggregates features
- Patient aggregation → Survival validation: validates survival
- Patient aggregation → Ligand-receptor screen: screens interactions
- Patient aggregation → Priority scoring: ranks targets
- Priority scoring → Bootstrap stability: tests stability
- Bootstrap stability → Analysis results: produces results
- Survival validation → Analysis results: produces results
- Ligand-receptor screen → Analysis results: produces results
- Analyst → Results dashboard: opens
- Analysis results → Results dashboard: summarized by