End-to-end snRNA-seq analysis of fibrolamellar carcinoma (FLC) tumor samples — includes QC, Harmony batch integration, and CellChat cell-cell communication analysis
Fibrolamellar carcinoma (FLC) is a rare primary liver cancer affecting adolescents and young adults. This project applies single-nucleus RNA-seq to characterize the cellular composition and communication landscape of FLC tumors, with the goal of identifying disease-relevant cell populations and rewired signaling pathways.
The analysis is organized as a series of R Markdown (.Rmd) documents, designed to be run sequentially:
| Step | Description |
|---|---|
| 1. QC | Ambient RNA removal, doublet detection, per-sample quality filtering |
| 2. Clustering | Dimensionality reduction (PCA, UMAP), graph-based clustering |
| 3. Cell type identification | Marker-based annotation of cell populations |
| 4. Harmony integration | Batch correction and cross-sample integration using Harmony |
| 5. CellChat analysis | Inference of cell-cell communication networks and signaling pathways |
- Input: Raw count matrices from 10x Chromium single-nucleus RNA-seq
- Samples: FLC tumor samples (Khashayar lab cohort)
Farghli, A. R., Chan, M., Sherman, M. S., et al. (2024). Single-cell multi-omic analysis of fibrolamellar carcinoma reveals rewired cell-to-cell communication patterns and unique vulnerabilities. bioRxiv.
Alaa R. Farghli — LinkedIn | Google Scholar | ORCID