What problem does it solve? Analyzing chromatin accessibility from 10x Multiome RNA+ATAC data requires coordinating many specialized steps — fragment loading, TSS enrichment QC, TF-IDF/LSI reduction, WNN integration, motif analysis, and peak-gene linkage — and mistakes like using a depth-correlated LSI component silently corrupt downstream results. ## Core Features & Use Cases - Multiome QC and preprocessing: Load 10x Cell Ranger outputs into a Seurat object with a ChromatinAssay, compute nucleosome signal and TSS enrichment, and filter low-quality cells. - Joint RNA+ATAC analysis: Run TF-IDF + LSI on peaks, SCTransform + PCA on RNA, and integrate both modalities with weighted nearest neighbors (WNN). - Regulatory genomics: Compute gene activity scores, differential accessibility with logistic regression, ChromVAR motif enrichment with JASPAR, peak-gene linkage, and locus-level coverage plots. - Use Case: Given a 10x Multiome experiment on PBMCs, build a WNN UMAP, identify B-cell vs T-cell differential peaks, and visualize CTCF motif activity and MS4A1 locus coverage. ## Quick Start Use the Signac workflow to load my filtered_feature_bc_matrix.h5 and atac_fragments.tsv.gz files, run QC and WNN integration, and produce a coverage plot for the MS4A1 locus.
