prehensilecode/regenie-apptainer

Recipe for building an Apptainer to run Regenie

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statgen/locuszoom

A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

Language: JavaScript - Size: 14.8 MB - Last synced at: 17 days ago - Pushed at: 21 days ago - Stars: 160 - Forks: 30

ShujiaHuang/qmplot

A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.

Language: Python - Size: 2.36 MB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 45 - Forks: 11

lcrawlab/mvMAPIT

The multivariate MArginal ePIstasis Test

Language: R - Size: 37.8 MB - Last synced at: 5 days ago - Pushed at: 7 months ago - Stars: 12 - Forks: 1

jennasimit/flashfmZero

Latent factor GWAS; Multi-trait fine-mapping for any number of uncorrelated traits (and limited number of correlated traits)

Language: R - Size: 7.33 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

katiesaund/hogwash

Three bacterial GWAS methods all rolled into one easy-to-use R package

Language: R - Size: 11.8 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 20 - Forks: 5

lcrawlab/sme

A fast and scalable method to detect epistasis in complex traits from biobank-scale studies

Language: C++ - Size: 3.25 MB - Last synced at: 10 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

GreallyLab/gaiaAssociation

gaiaAssociation is a tool to detect the cell specific enrichment of loci in regulatory regions through the sum of non-identical binomials

Language: Python - Size: 505 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 1

YADengUU/censGWAS

Perform GWAS on Phenotype Measurements Subject to Limit of Detection for Biobank-Scale Dataset

Language: R - Size: 312 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

lcrawlab/i-LDSC

Code and simulations using interaction-LD score regression

Language: Python - Size: 15.4 GB - Last synced at: 6 months ago - Pushed at: 11 months ago - Stars: 12 - Forks: 1

statgen/zorp

A simple GWAS parser + CLI

Language: Python - Size: 454 KB - Last synced at: 27 days ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

matthijsknigge/mendelianrandomization

MendelianRandomization is an R package for assessing causal relationships using genetic variants as instrumental variables

Language: R - Size: 901 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 2 - Forks: 0

fl-yu/SCAVENGE-dev

SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.

Language: R - Size: 35.3 MB - Last synced at: 12 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

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)

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BorgwardtLab/HOGImine

Higher-order genetic interaction discovery with network-based biological priors.

Language: C++ - Size: 49.8 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 1

statgen/localzoom

Make interactive LocusZoom plots from a local GWAS file

Language: Vue - Size: 5.76 MB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 7 - Forks: 4

ramachandran-lab/ESNN

Code and simulations using an Ensemble of Single-Effect Neural Networks (ESNN)

Language: Python - Size: 5.38 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 1

genetics-statistics/faster_lmm_d

A faster lmm for GWAS. Supports GPU backend.

Language: D - Size: 46.3 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 13 - Forks: 6

akcorut/kGWASflow

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Language: Python - Size: 610 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 24 - Forks: 5

statgen/locuszoom-hosted

A web service to upload and share GWAS results with LocusZoom.js

Language: Python - Size: 3.42 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

Snitkin-Lab-Umich/prewas

R package to perform data pre-processing for more informative bacterial GWAS

Language: R - Size: 927 KB - Last synced at: about 2 months ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 3

DGU-CBLAB/MEGASOFT

MEGASOFT

Language: C++ - Size: 114 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

EpistasisLab/regens

Recombines real genomic segments to simulate whole genomes

Language: Python - Size: 206 MB - Last synced at: 5 days ago - Pushed at: about 4 years ago - Stars: 4 - Forks: 2

snaketron/genphen

Tool for genome wide association studies with Bayesian inference and statistical learning

Language: R - Size: 49.5 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 2

RayDebashree/GWAStools

A curated list (with links) of useful tools for genome-wide association analysis.

Size: 4.88 KB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 7 - Forks: 4

HaohanWang/CMM

Coupled Mixed Model

Language: Python - Size: 8.26 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 3

hagax8/PathAnalyzor

Just another wrapper for pathway analysis using MAGMA

Language: Shell - Size: 28.4 MB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

maya123z/DGRP-Cleanup

Clean and Process GWAS Results for the Drosophila Genetic Reference Panel

Language: R - Size: 22.5 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

antoniogomez/UVIC_TFM_AGomez_2023

Scripts of Final Master Project

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lorinanthony/MAPIT

Code and Tutorials for Running the MArginal ePIstasis Test (MAPIT)

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npredey/GeneticAncestryTool

Language: Python - Size: 34.5 MB - Last synced at: about 2 months ago - Pushed at: about 7 years ago - Stars: 3 - Forks: 3

esohkevin/gwas-tips

tips and tricks in genome-wide association studies - a tutorial

Size: 19.1 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 9 - Forks: 8

RayDebashree/PLACO

A statistical test of pleiotropic effect of a genetic variant on two traits using GWAS summary statistics

Language: R - Size: 164 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 14 - Forks: 4

lcrawlab/BANNs

Code and simulations using biologically annotated neural networks

Language: HTML - Size: 22 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 20 - Forks: 3

medical-genomics-group/gmrm

A Bayesian grouped mixture of regressions model capable of estimating SNP marker effect sizes for multiple outcomes simultaneously

Language: C++ - Size: 61.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 1

lightning-auriga/statgen-mi

multiple imputation for association studies

Language: Python - Size: 10.9 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

RayDebashree/GxE

Joint meta-analysis of 2-df gene and gene-environment tests in GWAS.

Language: R - Size: 33.2 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

RayDebashree/TDT-like-tests

Modified transmission disequilibrium test (TDT) for GWAS using case-parent/control-parent trios.

Language: R - Size: 28.3 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

RayDebashree/mvtests

mvtests: a suite of functions for testing genetic associations of multiple traits (a.k.a. cross-phenotype associations)

Language: R - Size: 335 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 1

rcorty/wISAM

weighted GWAS (heteroskedastic GWAS)

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luisgarreta/multiGWAS

MultiGWAS tool for Genome-Wide Association Studies (GWAS) in plants (diploide and tetraploide)

Language: HTML - Size: 169 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

Zepeng-Mu/qqman Fork of stephenturner/qqman

This is a fork from qqman package

Language: R - Size: 16.2 MB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 1

sinarueeger/ggGWAS

R package 📦 with ggplot2 extensions for GWAS summary statistics (still in 🚧)

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