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