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A protein Quantitative Trait Locus toolkit

It seeds collection of data and utilties for pQTL analysis. At this early stage, the repository contains 1. a number of protein panels, linking functions for cis/trans classification, 2D Manhattan plots, 3D-plotly plots, forest plots among others availale from R/gap; 2. query on genes, regions, and SNPs via PhenoScanner, adding functionality to check for replication across platforms; 3. downstream analysis such as colocalization, pQTL-Mendelian Randomization via TwoSampleMR, linkage through UniProt IDs to other resources; 4. showcase of Bioconductor packages and snakemake workflow.

Aspects involving data from ongoing project have been simplified to use files in ~/pQTLtools/testswhich can be made public when appropriate.


The latest version of pQTLtools can be installed as usual:


Dependencies are detailed in the DECRIPTION file of the package at GitHub.

June 2022 update

It passes CRAN checks with no warning.

February 2021 update

A web-driven documentation is now available.

A summary of datasets and functions

This can be seen from R with