gwas-tools
There are 41 repositories under gwas-tools topic.
statgen/locuszoom
A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.
ShujiaHuang/qmplot
A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.
akcorut/kGWASflow
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
RayDebashree/PLACO
A statistical test of pleiotropic effect of a genetic variant on two traits using GWAS summary statistics
lcrawlab/BANNs
Code and simulations using biologically annotated neural networks
katiesaund/hogwash
Three bacterial GWAS methods all rolled into one easy-to-use R package
BorgwardtLab/HOGImine
Higher-order genetic interaction discovery with network-based biological priors.
esohkevin/gwas-tips
tips and tricks in genome-wide association studies - a tutorial
genetics-statistics/faster_lmm_d
A faster lmm for GWAS. Supports GPU backend.
lorinanthony/MAPIT
Code and Tutorials for Running the MArginal ePIstasis Test (MAPIT)
lcrawlab/i-LDSC
Code and simulations using interaction-LD score regression
RayDebashree/GWAStools
A curated list (with links) of useful tools for genome-wide association analysis.
lcrawlab/mvMAPIT
The multivariate MArginal ePIstasis Test
medical-genomics-group/gmrm
A Bayesian grouped mixture of regressions model capable of estimating SNP marker effect sizes for multiple outcomes simultaneously
naim-panjwani/LocusFocus
Application of the Simple Sum method for testing co-localization of GWAS with any other SNP-level data (e.g. eQTL data)
statgen/localzoom
Make interactive LocusZoom plots from a local GWAS file
HaohanWang/CMM
Coupled Mixed Model
Snitkin-Lab-Umich/prewas
R package to perform data pre-processing for more informative bacterial GWAS
EpistasisLab/regens
Recombines real genomic segments to simulate whole genomes
ramachandran-lab/ESNN
Code and simulations using an Ensemble of Single-Effect Neural Networks (ESNN)
snaketron/genphen
Tool for genome wide association studies with Bayesian inference and statistical learning
GreallyLab/gaiaAssociation
gaiaAssociation is a tool to detect the cell specific enrichment of loci in regulatory regions through the sum of non-identical binomials
sinarueeger/ggGWAS
R package 📦 with ggplot2 extensions for GWAS summary statistics (still in 🚧)
jennasimit/flashfm
Flashfm: multi-trait fine-mapping that uses GWAS summary statistics from several traits
jennasimit/MGflashfm
MGflashfm: joint fine-mapping of genetic association signals in several traits amongst multiple population groups.
RayDebashree/mvtests
mvtests: a suite of functions for testing genetic associations of multiple traits (a.k.a. cross-phenotype associations)
abought/zorp
A simple GWAS parser + CLI
hagax8/PathAnalyzor
Just another wrapper for pathway analysis using MAGMA
matthijsknigge/mendelianrandomization
MendelianRandomization is an R package for assessing causal relationships using genetic variants as instrumental variables
statgen/locuszoom-hosted
A web service to upload and share GWAS results with LocusZoom.js
Zepeng-Mu/qqman
This is a fork from qqman package
antoniogomez/UVIC_TFM_AGomez_2023
Scripts of Final Master Project
luisgarreta/multiGWAS
MultiGWAS tool for Genome-Wide Association Studies (GWAS) in plants (diploide and tetraploide)
RayDebashree/TDT-like-tests
Modified transmission disequilibrium test (TDT) for GWAS using case-parent/control-parent trios.
fl-yu/SCAVENGE-dev
SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.