Ravi Shanker Pandey, Ph.D. Associate Computational Scientist | The Jackson Laboratory
Complete scATAC-seq analysis of 10x Genomics PBMC data using Signac — from raw fragment files through QC, dimensionality reduction, clustering, gene activity scoring, and cell type annotation.
- 4,560 high-quality cells after QC filtering
- 11 clusters → 6 immune cell types identified
- LSI_1 excluded (correlated with sequencing depth)
- Cell types: CD4 T, CD8 T, NK, B cells, Monocytes, Dendritic cells
Fragment file → Peak matrix → QC filtering → TF-IDF normalization → LSI/SVD → DepthCor (exclude LSI_1) → UMAP → Leiden clustering → Gene activity scores → Cell type annotation
| Metric | Cutoff | Result |
|---|---|---|
| % Reads in peaks | >15% | Median 75% ✅ |
| Blacklist ratio | <0.05 | ~0.000 ✅ |
| Nucleosome signal | <4 | Median 0.57 ✅ |
| TSS enrichment | >2 | Median 6.19 ✅ |
library(Signac) # >= 1.17
library(Seurat) # >= 5.0
library(EnsDb.Hsapiens.v86)
library(biovizBase)| Repository | Description |
|---|---|
| sea-ad-microglia-analysis | scVI + trajectory |
| spatial-brain-deconvolution | Visium + RCTD |