Create a paired RNA/ATAC object
Build one Seurat object with matched RNA and Signac ATAC assays and check cell matching.
Paired RNA/ATAC notebooks for object construction, weighted nearest neighbors, peak–gene linkage, and label transfer.
Paired RNA/ATAC weighted nearest neighbors
Build RNA and ATAC representations, combine them with weighted nearest neighbors, and cluster the paired object.
RNA–ATAC peak–gene linkage
Use Signac LinkPeaks to estimate associations between RNA expression and nearby ATAC peaks.
RNA-to-ATAC label transfer
Transfer labels from an RNA reference to an ATAC query through GeneActivity and shared gene-space anchors.