Distinguishing causal from tagging enhancers using single-cell multiome data

The below data are associated with our paper entitled "Distinguishing causal from tagging enhancers using single-cell multiome data." See the Methods section of the paper for additional details. The .tar.gz archive contains 3 folders: 1) peak_scores/: Peak-level scores (co-accessibility score, co-activity score) computed for all ATAC peaks in 7 scRNA+ATAC-seq data set-cell type pairs. Files are labeled as: <dataset>_<cell_type>_peak_scores.tsv. Description of columns: peak: ATAC-seq peak coaccessibility_score: co-accessibility score genome_wide_coaccessibility_score: genome-wide co-accessibility score coactivity_score: co-activity score genome_wide_coactivity_score: genome-wide co-activity score 2) gene_scores/: Gene-level scores (gene co-expression score, gene co-activity score) computed for all genes in 7 scRNA+ATAC-seq data set-cell type pairs. Files are labeled as: <dataset>_<cell_type>_gene_scores.tsv. Description of columns: gene: gene gene_coexpression_score: gene co-expression score genome_wide_gene_coexpression_score: genome-wide co-expression score gene_coactivity_score: gene co-activity score genome_wide_gene_coactivity_score: genome-wide gene co-activity score 3) finemapped_peak_gene_linking_scores/: Peak-gene linking scores in 7 scRNA+ATAC-seq data set-cell type pairs generated by existing methods ArchR (Granja et al. 2021 Nat Genet) and Signac (Stuart et al. 2021 Nat Methods, Ma et al. 2020 Cell), including marginal linking scores and fine-mapped scores. Files are labeled as: <dataset>_<cell_type>_<method>_finemapped_peak_gene_linking_scores.tsv. Description of columns: peak: ATAC peak in candidate peak-gene pair gene: Gene in candidate peak-gene pair Marginal: marginal linking score (squared correlation from ArchR or Signac) SCP: single causal peak fine-mapped linking score SCP+Functional: functionally-informed single causal peak fine-mapped linking score MCP: multiple causal peak fine-mapped linking score MCP+Functional: functionally informed multiple causal peak fine-mapped linking score *NOTE: linking predictions span candidate links with peak-gene distance <1Mb, excluding promoters (+/- 1kb from TSS) (see manuscript)*