eqtl

LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.

Experimental design framework for scRNAseq population studies (eQTL and DE)

Software to perform multi-ancestry SNP fine-mapping on molecular data

Using real genotype data, simulate a complex trait as a function of latent expression, fit eQTL weights in independent data, and perform GWAS/TWAS on complex trait.

CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

Script and pipeline for BRAINcode project

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Older repo for MRLocus. See new website for software usage guide:

NPDR: Nearest-neighbor Projected-Distance Regression with the generalized linear model

An R interface to the GTEx Portal API

Tejaas - a tool for discovering trans-eQTLs

Application of the Simple Sum method for testing co-localization of GWAS with any other SNP-level data (e.g. eQTL data)

Analysis of regulatory impacts of autism-associated SNPs on biological pathways in the fetal and adult cortex.

Analysis of regulatory impacts of GWAS SNPs associated with psychiatric disorders and cognitive functioning.

Trait association analyses on the Human Pangenome Reference

METAINFORMANT is a Python 3.11+ multi-omic bioinformatics toolkit spanning 28 modules and 650+ files for DNA, RNA-seq, protein, epigenome and single-cell analysis, GWAS with fine-mapping and eQTL, joint PCA, 70+ plot types — uv-managed, 7,700+ tests, demoed on 8,300+ samples across 28 species.

Computationally efficient and statistically powerful software for detecting context-specific eQTL effects in multi-context genomic studies.

A workflow based on QTLtools to run cis- and trans-QTL analyses.

Computational biology/bioinformatics workflows, codes, tech & concept notes on NGS data