CatalogueR

<img src='https://github.com/RajLabMSSM/catalogueR/raw/master/inst/hex/hex.png' title='Hex sticker for catalogueR' height='300'><br> <br> <br> <a href='https://app.codecov.io/gh/RajLabMSSM/catalogueR/tree/master' target='_blank'><img src='https://codecov.io/gh/RajLabMSSM/catalogueR/branch/master/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>

<h4> Authors: <i>Brian Schilder, Jack Humphrey, Towfique Raj</i> </h4>

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

<hr>

Contact

<a href="https://bschilder.github.io/BMSchilder/" target="_blank">Brian M. Schilder, Bioinformatician II</a>
<a href="https://rajlab.org" target="_blank">Raj Lab</a>
<a href="https://icahn.mssm.edu/about/departments-offices/neuroscience" target="_blank">Department of Neuroscience, Icahn School of Medicine at Mount Sinai</a>