eqtl
There are 3 repositories under eqtl topic.
boxiangliu / locuscomparer
LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.
Language:R 91- Language:R 41
mancusolab / twas_sim
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.
Language:Shell 23limix / CellRegMap
CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq
Language:Python 20single-cell-genetics / singlecell_neuroseq_paper
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
Language:Jupyter Notebook 19- Language:HTML 17
- Language:R 16
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
Language:Jupyter Notebook 15Software to perform multi-ancestry SNP fine-mapping on molecular data
Language:Python 13insilico / npdr
NPDR: Nearest-neighbor Projected-Distance Regression with the generalized linear model
Language:R 12soedinglab / tejaas
Tejaas - a tool for discovering trans-eQTLs
Language:C 9Genome3d / psychiatric_and_cognitive_multimorbidities
Analysis of regulatory impacts of GWAS SNPs associated with psychiatric disorders and cognitive functioning.
Language:HTML 8naim-panjwani / LocusFocus
Application of the Simple Sum method for testing co-localization of GWAS with any other SNP-level data (e.g. eQTL data)
Language:JavaScript 8BrunildaBalliu / FastGxC
Computationally efficient and statistically powerful software for detecting context-specific eQTL effects in multi-context genomic studies.
Language:R 7Analysis of regulatory impacts of autism-associated SNPs on biological pathways in the fetal and adult cortex.
Language:HTML 6swvanderlaan / QTLToolKit
A workflow based on QTLtools to run cis- and trans-QTL analyses.
Language:Shell 6dvav / eQTLseq
Hierarchical probabilistic models for multiple gene/variant associations based on NGS data
Language:Jupyter Notebook 5szcf-weiya / MTWAS
R package for "Multi-tissue Transcriptome-Wide Association Studies (MTWAS)"
Language:R 4Analysis of tissue-specific regulatory impacts of alcohol dependence-associated SNPs.
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RajLabMSSM / QTL-mapping-pipeline
A snakemake pipeline for QTL mapping. Based on the GTEX pipeline
Language:Python 3- Language:MATLAB 2
senresearch / LiteQTL.jl
A lightweight Julia package for eQTL genome scans near real-time.
Language:Jupyter Notebook 2- Language:R 2
- Language:R 2
fastQTL analysis of methylation and expression data
Language:Shell 2XUKEREN / phd-pipeline
Some workflows I wrote for my phd projects
Language:Shell 2Association analysis of ADH and ALDH gene regulatory interactions with GWAS traits.
Language:HTML 1JunWangmath / GeP-HMRF
Hidden Markov Random Field Model - Inferring Gene-Disease Association by an Integrative Analysis of eQTL GWAS and Protein-Protein Interaction data
Language:R 1NCBI-Hackathons / chromatinonlinedatabase
An Online Database of 3D Chromatin Structure
Language:PHP 1- Language:R 1
- UVIC_TFM_AGomez_2023
antoniogomez / UVIC_TFM_AGomez_2023
Scripts of Final Master Project
Language:R 0 De novo discovery of traits co-occurring with chronic obstructive pulmonary disease.
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- Language:Jupyter Notebook 0
- Language:Python
