catalogueR: Rapid querying, colocalization, and plotting of summary stats from the eQTL Catalogue. 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
if(!require("remotes")) install.packages("remotes")
remotes::install_github("RajLabMSSM/catalogueR")
library(catalogueR)-
The functions in
catalogueRare 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:https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv
Brian
M. Schilder, Bioinformatician II
Raj Lab
Department
of Neuroscience, Icahn School of Medicine at Mount Sinai