It seeds collection of data and utilities for pQTL analysis. At this early stage, the repository contains 1. Articles linking functions for cis/trans classification, 2d Manhattan plots, 2d/3d-plotly plots, forest plots among others available from 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. Bioconductor notes and a showcase of 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: