signac

HSC scATACseq analysis

scRNA-seq and scATAC-seq utilities

Reproducible benchmark reranking Signac LinkPeaks candidate peak–gene links from PBMC multiome data, with SCENT validation and explicit promoter-proximity controls.

Complete scATAC-seq analysis of PBMC data using Signac — QC, TF-IDF normalization, LSI dimensionality reduction, clustering, gene activity scoring and cell type annotation

snRNA+snATAC multiome of AD DLPFC microglia — chromVAR motif analysis, WNN integration, peak-to-gene linkage, Monocle3 trajectory | Signac · Seurat · R

The standard pipeline for single-cell ATAC-seq analysis using Signac in R, covering preprocessing, QC, dimensionality reduction, and clustering.

scATAC-seq pipeline mapping mucosal immunity and host-microbe crosstalk. Profiles physical chromatin accessibility of Trm cells (Itgae/CD103) and Secretory IgA Plasma cells (Igj) to decode intestinal defense mechanisms.