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BST1
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echolocatoR output example (BST1 locus) |
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BST1__Alasoo_2018.macrophage_IFNg
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eQTL Catalogue query results |
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LRRK2
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echolocatoR output example (LRRK2 locus) |
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LRRK2__Alasoo_2018.macrophage_IFNg
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eQTL Catalogue query results |
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MEX3C
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echolocatoR output example (MEX3C locus) |
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MEX3C__Alasoo_2018.macrophage_IFNg
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eQTL Catalogue query results |
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catalogueR-package
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Rapid querying, colocalization, and plotting of summary stats from the eQTL Catalogue |
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coloc_QTLs
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Example colocalization results |
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coloc_QTLs_full
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Example colocalization results |
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eQTL_Catalogue.annotate_tissues()
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Annotate QTL datasets with metadata |
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eQTL_Catalogue.fetch()
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2. Query eQTL Catalogue datasets by region |
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eQTL_Catalogue.header
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eQTL Catalogue tabix header |
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eQTL_Catalogue.iterate_fetch()
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Iterate queries to eQTL Catalogue |
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eQTL_Catalogue.list_datasets()
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List available eQTL datasets |
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eQTL_Catalogue.query()
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Iterate queries to eQTL Catalogue |
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eQTL_Catalogue.search_metadata()
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Search eQTL Catalogue metadata |
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ensembl_to_hgnc()
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Convert ENSEMBL IDs to HGNC gene symbols |
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example_eQTL_Catalogue_query_paths()
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Paths to example eQTL Catalogue query results |
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example_sumstats_paths()
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Paths to example summary stats |
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fetch_restAPI()
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2. Query eQTL Catalogue datasets by region |
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fetch_tabix()
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2. Query eQTL Catalogue datasets by region |
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find_consensus_SNPs()
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Find Consensus SNPs in echolocatoR output |
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gather_colocalized_data()
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Prepare data for coloc plot |
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gather_files()
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Merge files from a list of paths |
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get_colocs()
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Run coloc on GWAS-QTL object |
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hgnc_to_ensembl()
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Convert HGNC gene symbols to ENSEMBL IDs |
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liftover()
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Lift genome across builds |
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merge_gwas_qtl()
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Merge GWAS data (query) and QTL data (results) |
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meta
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eQTL Catalogue dataset metadata |
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multi_locus_plot()
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Faceted Manhattan plots of QTL datasets |
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plot_coloc_summary()
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Plot summary of coloc tests |
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retrieve_sumstats_info()
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Merge coloc results with SNP-wise GWAS/QTL data |
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run_coloc()
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Iteratively run coloc on merged GWAS-QTL datatables |