Modules:
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candidate_selection–Candidate (trait locus, protein) pairs for colocalization, and their selection within a budget.
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coloc_abf–Colocalization of two traits at one locus by approximate Bayes factors (coloc.abf).
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coloc_display_table_task–Docs-facing table of the colocalizations of one trait with proteins.
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coloc_locus_plot_task–Stacked locus plots of chosen trait x protein colocalizations.
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coloc_locus_stack_plot_task–Stacked locus plots of the colocalizing proteins at each locus of a coloc display table.
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coloc_protein_info_task–Annotations of the colocalizing proteins at the top loci of a coloc display table, from static
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csf_gene_coords_reader–Gene coordinates for the Western et al. 2024 CSF aptamers: each aptamer's NCBI Entrez gene id
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csf_window_fetcher–DenseWindowFetcher for the Western et al. 2024 CSF pQTL GWAS: reads trait-locus windows of one
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gene_coords_reader–Source-specific readers turning a gene-coordinate table into the map protein id -> GRCh38
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orient_and_align–Orient a dense protein window to the reference genome and align it exactly to the trait.
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ppp_window_fetcher–Fetch dense protein summary statistics for a few locus windows, then discard the download.
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protein_accessions_reader–Source-specific readers turning a proteomics source's protein table into the UniProt accessions
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protein_hit_table_task–Table of genome-wide significant hit segments for every protein of a proteomics GWAS
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trait_loci–Genome-wide significant loci of a trait, as windows around lead variants.
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trait_protein_coloc_task–Colocalize one trait GWAS with every proteomics GWAS that has a hit at one of its loci.