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analysis_code_for_mpra

Used codes to detect allelic effect on MPRA data

dap

software package for integrative genetic association analysis

dpolyqtl

gemma

Genome-wide Efficient Mixed Model Association

mmqtl

MMQTL is a statistical package applying meta-analysis to detect multiple QTL signals integrating signals among conditions, with control for population structure and relatedness

multi-eqtl_polygeneic

For this package, I'm trying to develop a Bayesian method to perform multiple eQTL detection with a control for population structure or relatedness when the phenotype has a polygenetic background

parallel_caviar

In current version of CAVIAR (https://github.com/fhormoz/caviar), it runs in a serial manner. To speed up the running, I convert it to a parallel version, which applies openmp to run with multi-thread. Simulation results demonstrate that when explored variants are massive, the running time is only 1/nthread of original version.

polyqtl

A Bayesian method performing multiple eQTL detection with a control for population structure and relatedness

script-for-constraint-paper

This repository contains scripts that I used to perform simulation with CAGE genotype to demonstrate the interference between multiple causal variants when conducting eQTL detection