To demonstrate the core functionality of the Signac package we analyzed a publicly available dataset that jointly profiled messenger RNA abundance and DNA accessibility in single human peripheral blood mononuclear cells (PBMCs), generated by 10x Genomics. We computed per-cell quality control (QC) metrics using the DNA accessibility assay, including the strength of the nucleosome banding pattern (Fig. 2a) and transcriptional start site (TSS) enrichment score (Fig. 2b; Methods) and removed low-quality cells based on these QC metrics resulting in a dataset of 10,466 cells. Next, we processed the gene expression assay by normalizing RNA counts with SCTransform and Seurat41,45. We annotated cell types by mapping cells to an annotated multimodal PBMC reference dataset, using the gene expression assay42. This revealed 20 different cell types present in the dataset, including rare populations such as γδ T cells.
