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)

Trait association analyses on the Human Pangenome Reference

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.

METAINFORMANT is a Python multi-omic bioinformatics toolkit for DNA, RNA-seq, protein, epigenome and single-cell analysis, GWAS with fine-mapping and eQTL, joint PCA and a broad plot-type library — uv-managed and tested, demoed on multi-species sample data.

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

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

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