Authors: Brian Schilder, Jack Humphrey, Towfique Raj

catalogueR: Rapid querying, colocalization, and plotting of summary stats from the eQTL Catalogue https://www.ebi.ac.uk/eqtl/. eQTL Catalogue currently contains >100 datasets from 20 different studies (including GTEx), across many tissues/cell types/conditions.

This R package is part of the echoverse suite that supports echolocatoR: an automated genomic fine-mapping pipeline.

If you use catalogueR, please cite:

and

N Kerimov, JD Hayhurst, K Peikova, et al. A compendium of uniformly processed human gene expression and splicing quantitative trait loci. Nat Genet 53, 1290–1299 (2021). https://doi.org/10.1038/s41588-021-00924-w

Installation

if(!require("BiocManager")) install.packages("BiocManager")

BiocManager::install("RajLabMSSM/catalogueR")
library(catalogueR)

Documentation

Website

Getting started

Notes

• The functions in catalogueR are partly derived from the eQTL Catalogue tutorial.

• The ALT allele is always the effect allele in eQTL Catalogue.

• Additional eQTL Catalogue resources:

  • GitHub repository
  • In-depth API documentation
  • FTP server: ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv

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Contact

Brian M. Schilder, Bioinformatician II
Raj Lab
Department of Neuroscience, Icahn School of Medicine at Mount Sinai