| _version_ | 1866901964764217344 |
|---|---|
| author | Dorans, Elizabeth |
| author_facet | Dorans, Elizabeth |
| contents | <p>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.</p> <p>The .tar.gz archive contains 3 folders:</p> <p>1) <strong>peak_scores/</strong>: 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: <strong><dataset>_<cell_type>_peak_scores.tsv</strong>.</p> <p>Description of columns:</p> <ul> <li>peak: ATAC-seq peak</li> <li>coaccessibility_score: co-accessibility score</li> <li>genome_wide_coaccessibility_score: genome-wide co-accessibility score</li> <li>coactivity_score: co-activity score</li> <li>genome_wide_coactivity_score: genome-wide co-activity score</li> </ul> <p>2) <strong>gene_scores/</strong>: 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: <strong><dataset>_<cell_type>_gene_scores.tsv</strong>.</p> <p>Description of columns:</p> <ul> <li>gene: gene</li> <li>gene_coexpression_score: gene co-expression score</li> <li>genome_wide_gene_coexpression_score: genome-wide co-expression score</li> <li>gene_coactivity_score: gene co-activity score</li> <li>genome_wide_gene_coactivity_score: genome-wide gene co-activity score</li> </ul> <p>3) <strong>finemapped_peak_gene_linking_scores/:</strong><strong> </strong>Peak-gene linking scores in 7 scRNA+ATAC-seq data set-cell type pairs generated by existing methods ArchR (Granja et al. 2021 <em>Nat Genet</em>) and Signac (Stuart et al. 2021 <em>Nat Methods, </em>Ma et al. 2020 <em>Cell</em>), including marginal linking scores and fine-mapped scores. Files are labeled as: <strong><dataset>_<cell_type>_<method>_finemapped_peak_gene_linking_scores.tsv</strong>.</p> <p>Description of columns:</p> <ul> <li>peak: ATAC peak in candidate peak-gene pair</li> <li>gene: Gene in candidate peak-gene pair</li> <li>Marginal: marginal linking score (squared correlation from ArchR or Signac)</li> <li>SCP: single causal peak fine-mapped linking score</li> <li>SCP+Functional: functionally-informed single causal peak fine-mapped linking score </li> <li>MCP: multiple causal peak fine-mapped linking score </li> <li>MCP+Functional: functionally informed multiple causal peak fine-mapped linking score </li> </ul> <p><em>*NOTE: linking predictions span candidate links with peak-gene distance <1Mb, excluding promoters (+/- 1kb from TSS) (see manuscript)*</em></p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18643360 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Distinguishing causal from tagging enhancers using single-cell multiome data Dorans, Elizabeth <p>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.</p> <p>The .tar.gz archive contains 3 folders:</p> <p>1) <strong>peak_scores/</strong>: 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: <strong><dataset>_<cell_type>_peak_scores.tsv</strong>.</p> <p>Description of columns:</p> <ul> <li>peak: ATAC-seq peak</li> <li>coaccessibility_score: co-accessibility score</li> <li>genome_wide_coaccessibility_score: genome-wide co-accessibility score</li> <li>coactivity_score: co-activity score</li> <li>genome_wide_coactivity_score: genome-wide co-activity score</li> </ul> <p>2) <strong>gene_scores/</strong>: 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: <strong><dataset>_<cell_type>_gene_scores.tsv</strong>.</p> <p>Description of columns:</p> <ul> <li>gene: gene</li> <li>gene_coexpression_score: gene co-expression score</li> <li>genome_wide_gene_coexpression_score: genome-wide co-expression score</li> <li>gene_coactivity_score: gene co-activity score</li> <li>genome_wide_gene_coactivity_score: genome-wide gene co-activity score</li> </ul> <p>3) <strong>finemapped_peak_gene_linking_scores/:</strong><strong> </strong>Peak-gene linking scores in 7 scRNA+ATAC-seq data set-cell type pairs generated by existing methods ArchR (Granja et al. 2021 <em>Nat Genet</em>) and Signac (Stuart et al. 2021 <em>Nat Methods, </em>Ma et al. 2020 <em>Cell</em>), including marginal linking scores and fine-mapped scores. Files are labeled as: <strong><dataset>_<cell_type>_<method>_finemapped_peak_gene_linking_scores.tsv</strong>.</p> <p>Description of columns:</p> <ul> <li>peak: ATAC peak in candidate peak-gene pair</li> <li>gene: Gene in candidate peak-gene pair</li> <li>Marginal: marginal linking score (squared correlation from ArchR or Signac)</li> <li>SCP: single causal peak fine-mapped linking score</li> <li>SCP+Functional: functionally-informed single causal peak fine-mapped linking score </li> <li>MCP: multiple causal peak fine-mapped linking score </li> <li>MCP+Functional: functionally informed multiple causal peak fine-mapped linking score </li> </ul> <p><em>*NOTE: linking predictions span candidate links with peak-gene distance <1Mb, excluding promoters (+/- 1kb from TSS) (see manuscript)*</em></p> |
| title | Distinguishing causal from tagging enhancers using single-cell multiome data |
| url | https://doi.org/10.5281/zenodo.18643360 |