The manuscript is currently under review by Genome Biology. Please check out the preprint at https://www.medrxiv.org/content/10.64898/2026.02.05.26345013v1.
- LDSC workflow: used to assess trait heritability partitioned by different functional annotations
- scE2G workflow: used to identify enhancer-to-gene links from single-cell multiome data
- Processing scRNA-seq datasets:
- scRNA_dublets_removal.ipynb
- scRNA_seq_integration_Seurat.ipynb
- validate_cell_type_annotations.ipynb
- cross-tissue_differential_gene_expression.ipynb
- Processing scATAC-seq datasets:
- analyze_scATAC_seq_ArchR.ipynb
- validate_cell_type_annotations_with_ATAC-seq.Rmd
- Interpreting hertiability enrichment results
- heritability_enrichment_for_lung_OCRs.Rmd
- Interpreting scE2G results and link them to asthma genetics
- link_CREs_to_genes.Rmd
- summarize_candidate_genes_43CREs.Rmd
- make_locus_plots.Rmd
- Interpreting GRN results and link them to asthma genetics
- GRN_plotting.ipynb
- TF_GRN_analysis.Rmd