Create a Signac scATAC object
Build a Seurat object with a Signac ChromatinAssay from peak counts, matching metadata, fragments, and genome annotation.
Signac notebooks for object construction, fragment-aware QC, TF-IDF/LSI, motif enrichment, and a chromVAR API reminder.
Fragment-aware scATAC quality control
Compute fragment-aware ATAC QC metrics, inspect them by sample, apply a baseline filter, and save the object.
TF-IDF, LSI, and clustering
Run the Signac TF-IDF, SVD, neighbor, clustering, and UMAP steps.
Motif enrichment with FindMotifs
Add JASPAR motif matches and test enrichment in a selected foreground peak set against a specified background universe.
chromVAR motif deviations
Give a minimal chromVAR reminder for estimating cell-level motif deviation scores.