omerwe/polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)

Language: Python - Size: 223 MB - Last synced: about 13 hours ago - Pushed: about 14 hours ago - Stars: 77 - Forks: 21

neurogenomics/phenomix

Explore the phenome ✨🎆✨

Language: R - Size: 61.7 MB - Last synced: about 13 hours ago - Pushed: 19 days ago - Stars: 0 - Forks: 0

dnanexus/UKB_RAP

Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.

Language: Jupyter Notebook - Size: 2.65 MB - Last synced: about 15 hours ago - Pushed: about 16 hours ago - Stars: 99 - Forks: 38

NCI-CGR/GwasQcPipeline

The CGR GWAS QC processing workflow.

Language: Python - Size: 86.7 MB - Last synced: about 19 hours ago - Pushed: about 21 hours ago - Stars: 0 - Forks: 1

jinghuazhao/Caprion

Caprion pilot study

Language: HTML - Size: 2.98 MB - Last synced: about 24 hours ago - Pushed: 1 day ago - Stars: 1 - Forks: 0

gorpipe/gor

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.

Language: Java - Size: 13.1 MB - Last synced: about 19 hours ago - Pushed: 1 day ago - Stars: 38 - Forks: 13

Alice-MacQueen/switchgrassGWAS

Genome-wide association on the Panicum virgatum diversity panel.

Language: R - Size: 60.2 MB - Last synced: 1 day ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

grimmlab/permGWAS

Efficient Permutation-based GWAS for Normal and Skewed Phenotypic Distributions

Language: Python - Size: 12.6 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 23 - Forks: 3

MRCIEU/opengwas-api

API for MRC-IEU OpenGWAS platform (https://gwas.mrcieu.ac.uk)

Language: Python - Size: 21 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 4 - Forks: 1

projectglow/glow

An open-source toolkit for large-scale genomic analysis

Language: Scala - Size: 96.7 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 259 - Forks: 105

ylaboratory/seismic

Seismic R package. Discover cell type-trait associations in minutes for GWAS and single-cell RNA-sequencing data

Language: R - Size: 45.1 MB - Last synced: 5 days ago - Pushed: 7 days ago - Stars: 0 - Forks: 0

pipaber/Multi-omics

This is a repository to show my experience analyzing different kinds of Omics data.

Language: JavaScript - Size: 5.46 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 0

BioPsyk/cleansumstats

Convert GWAS sumstat files into a common format with a common reference for positions, rsids and effect alleles.

Language: Shell - Size: 7.96 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 7 - Forks: 1

neurogenomics/MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

Language: R - Size: 8.7 MB - Last synced: about 13 hours ago - Pushed: 8 days ago - Stars: 64 - Forks: 14

ytakemon/1415-Col4a5xDO-Project

Scripts used for the 1415 Col4a5xDO project

Language: HTML - Size: 31.9 MB - Last synced: 8 days ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

ramiromagno/quincunx

quincunx: an R package to query, download and wrangle PGS Catalog data

Language: R - Size: 4.17 MB - Last synced: 9 days ago - Pushed: 10 months ago - Stars: 4 - Forks: 0

atgu/GWASpy

GWAS QC, PCA, haplotype phasing, genotype imputation

Language: Python - Size: 6.1 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 15 - Forks: 4

tatonetti-lab/indirect-gwas

Fast GWAS on linear combinations of traits using only summary statistics

Language: Rust - Size: 109 KB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 5 - Forks: 1

zietzm/igwas 📦

Fast GWAS on linear combinations of traits using only summary statistics - Rust re-implementation

Language: Rust - Size: 50.8 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 1 - Forks: 0

esohkevin/esohkevin.github.io

esohinformatics

Size: 25.1 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

jrazi/KnockoffOrigins

A Python implementation of the "Controlling the False Discovery Rate via Knockoffs" paper from 2015, designed to provide tools for generating knockoff features and applying controlled variable selection techniques in high-dimensional data settings.

Language: Python - Size: 66.4 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

omicsedge/selphi

weighted-PBWT genotype imputation algorithm

Language: Python - Size: 456 KB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 1 - Forks: 0

martinjzhang/scDRS

Single-cell disease relevance score (scDRS)

Language: Jupyter Notebook - Size: 196 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 92 - Forks: 11

tatonetti-lab/indirect-gwas-analysis

Accerating pan-biobank GWAS using phenotype projections

Language: Jupyter Notebook - Size: 5 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 1 - Forks: 0

shz9/magenpy

Modeling and Analysis of (Statistical) Genetics data in python

Language: Python - Size: 2.81 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 16 - Forks: 5

shz9/viprs

Variational Inference of Polygenic Risk Scores

Language: Python - Size: 9.36 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 15 - Forks: 0

mancusolab/sushie

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

Language: Python - Size: 922 KB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 13 - Forks: 2

nf-core/gwas

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

Language: Nextflow - Size: 2.69 MB - Last synced: about 21 hours ago - Pushed: about 22 hours ago - Stars: 19 - Forks: 16

mancusolab/FactorGo

Software to infer latent pleiotropic components from GWAS summary data

Language: Python - Size: 527 KB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 9 - Forks: 0

lcrawlab/i-LDSC

Code and simulations using interaction-LD score regression

Language: Python - Size: 15.4 GB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 8 - Forks: 1

folkehelseinstituttet/GWAS 📦

GWAS functionality

Language: R - Size: 51.8 KB - Last synced: 16 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 1

QuantGen/BGData

A Suite of Packages for Analysis of Big Genomic Data

Language: R - Size: 4.9 MB - Last synced: 14 days ago - Pushed: 8 months ago - Stars: 33 - Forks: 14

TohaRhymes/bioGWAS

Tool for GWAS simulations

Language: Jupyter Notebook - Size: 35.4 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 0

statgen/locuszoom

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

Language: JavaScript - Size: 15.5 MB - Last synced: 7 days ago - Pushed: about 1 year ago - Stars: 148 - Forks: 28

genepi/imputationserver

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

Language: Java - Size: 740 MB - Last synced: 17 days ago - Pushed: about 2 months ago - Stars: 72 - Forks: 38

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: 13 days ago - Pushed: 5 months ago - Stars: 33 - Forks: 11

swvanderlaan/GWASToolKit

A collection of scripts to run GWAS, regional, gene-oriented, or per-variant analyses.

Language: Shell - Size: 837 KB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 14 - Forks: 7

swvanderlaan/MetaGWASToolKit

A ToolKit to perform a Meta-analysis of Genome-Wide Association Studies

Language: Shell - Size: 477 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 12 - Forks: 2

CAST-genomics/haptools

Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis

Language: Python - Size: 8.21 MB - Last synced: about 2 hours ago - Pushed: about 1 month ago - Stars: 14 - Forks: 2

derekmichaelwright/gwaspr

An R package for plotting GWAS results from the GAPIT package

Language: HTML - Size: 171 MB - Last synced: 21 days ago - Pushed: 23 days ago - Stars: 4 - Forks: 0

neurogenomics/MAGMA_Celltyping

Find causal cell-types underlying complex trait genetics

Language: R - Size: 245 MB - Last synced: about 13 hours ago - Pushed: 7 months ago - Stars: 65 - Forks: 29

slowkow/snpsea

:bar_chart: Identify cell types and pathways affected by genetic risk loci.

Language: C++ - Size: 20.5 MB - Last synced: about 24 hours ago - Pushed: 2 months ago - Stars: 34 - Forks: 9

Jianhua-Wang/easyfinemap

user-friendly pipeline for GWAS fine-mapping

Language: Python - Size: 50.6 MB - Last synced: 22 days ago - Pushed: 23 days ago - Stars: 5 - Forks: 0

AhmedArslan/MRsimplify

TwosampleMR and MultivariableMR perform with simple commands without prior knowledge or having to go through lengthy boring protocols

Language: R - Size: 103 KB - Last synced: 23 days ago - Pushed: 24 days ago - Stars: 1 - Forks: 0

cyverseuk/GWASSER

Dockerized Agave app for GWASSER, an R script for simple gwassing.

Language: R - Size: 38.1 KB - Last synced: 23 days ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 1

comorment/containers

CoMorMent-Containers

Language: R - Size: 25.3 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 19 - Forks: 9

Cloufield/GWASTutorial

GWAS Tutorial for Beginners

Language: Jupyter Notebook - Size: 395 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 68 - Forks: 19

TileDB-Inc/TileDB-VCF

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Language: C++ - Size: 33 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 79 - Forks: 13

biona001/GhostKnockoffGWAS

Package for analyzing GWAS summary statistics data

Language: Julia - Size: 11.3 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 1 - Forks: 0

OpenMendel/OrdinalGWAS.jl

Genome-wide association studies (GWAS) for ordered categorical phenotypes

Language: Julia - Size: 3.86 MB - Last synced: 26 days ago - Pushed: 27 days ago - Stars: 20 - Forks: 7

opentargets/gentropy

Open Targets python framework for post-GWAS analysis

Language: Jupyter Notebook - Size: 18.8 MB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 20 - Forks: 4

aehrc/VariantSpark

machine learning for genomic variants

Language: JavaScript - Size: 74.5 MB - Last synced: 24 days ago - Pushed: 25 days ago - Stars: 138 - Forks: 44

shz9/tokyo-symposium-2024

Tokyo Symposium on Genomic Medicine (2024)

Language: Jupyter Notebook - Size: 1.5 MB - Last synced: 26 days ago - Pushed: 27 days ago - Stars: 3 - Forks: 0

sgkit-dev/sgkit

Scalable genetics toolkit

Language: Python - Size: 94.4 MB - Last synced: 25 days ago - Pushed: about 1 month ago - Stars: 213 - Forks: 33

mmkim1210/GeneticsMakie.jl

🧬High-performance genetics- and genomics-related data visualization using Makie.jl

Language: Julia - Size: 30.5 MB - Last synced: 22 days ago - Pushed: 2 months ago - Stars: 73 - Forks: 2

OpenMendel/MendelIHT.jl

Iterative hard thresholding for l0 penalized regression

Language: Julia - Size: 119 MB - Last synced: 12 days ago - Pushed: 8 months ago - Stars: 22 - Forks: 4

swvanderlaan/A_Practical_Primer_in_Human_Complex_Genetics

A Practical Primer in Human Complex Genetics

Language: Perl - Size: 259 MB - Last synced: 30 days ago - Pushed: 30 days ago - Stars: 2 - Forks: 0

Anacristina0914/GSA.Tissue.Celltype.Enrich

Repository containing source code, data, etc necessary to run Gene Set Analysis, Celltyping using MAGMA/Celltyping and Tissue Enrichment Analysis. Some of the formulas have been adapted from: NathanSkene/ALS_Human_EWCE, neurogenomics/EWCE, NathanSkene/MAGMA_Celltyping and jbryois/scRNA_disease github repositories.

Language: R - Size: 20.9 MB - Last synced: 16 days ago - Pushed: over 2 years ago - Stars: 3 - Forks: 1

ccb-hms/gwasCatSearch

tooling for semantic search of NHGRI GWAS catalog

Language: R - Size: 185 MB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 1

MartinKalema/Genomics-For-Alzheimer

Harnessing Genome Wide Association studies to identify biomarkers linked to the early onset of Alzheimer's disease and construct predictive models for the detection of these biomarkers within gene sequences.

Language: Python - Size: 9.77 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

MRCIEU/pygwasvcf

Python library for reading GWAS summary statistics in GWAS-VCF files

Language: Python - Size: 58.6 KB - Last synced: 5 days ago - Pushed: about 2 years ago - Stars: 6 - 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: about 1 month ago - Pushed: over 1 year ago - Stars: 4 - Forks: 1

Gregor-Mendel-Institute/gwaR

A collection of R functions to conduct downstream GWAS analysis for arabidopsis thaliana.

Language: R - Size: 389 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

chosenobih/Rice_GWAS_project

This repo houses the data, analysis scripts and results for our rice diversity panel drought induced oxidative stress enzymes and markers GWAS project

Size: 33.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

genetics-statistics/faster_lmm_d

A faster lmm for GWAS. Supports GPU backend.

Language: D - Size: 46.3 MB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 13 - Forks: 6

jgx65/hierfstat

the hierfstat package

Language: HTML - Size: 1000 KB - Last synced: 4 days ago - Pushed: about 1 year ago - Stars: 23 - Forks: 14

perslab/timshel-2020

Code to reproduce analysis and figures for 'Genetic mapping of etiologic brain cell types for obesity' (Timshel, eLife 2020)

Language: R - Size: 347 MB - Last synced: 24 days ago - Pushed: almost 3 years ago - Stars: 13 - Forks: 4

NCBI-Hackathons/MR_BACOn

Mendelian Randomization with Biomarker Associations for Causality with Outcomes

Language: R - Size: 29 MB - Last synced: 24 days ago - Pushed: over 5 years ago - Stars: 22 - Forks: 9

liangyy/silver-standard-performance

A light and flexible R package to evaluate GWAS-based gene prioritization methods for complex traits.

Language: R - Size: 4.29 MB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 3 - Forks: 3

Biometris/statgenGWAS

See https://biometris.github.io/statgenGWAS for a full description

Language: R - Size: 21.9 MB - Last synced: 5 days ago - Pushed: 3 months ago - Stars: 11 - Forks: 4

hail-is/hail

Cloud-native genomic dataframes and batch computing

Language: Python - Size: 118 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 925 - Forks: 235

BGI-shenzhen/LDBlockShow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files

Language: Perl - Size: 24.6 MB - Last synced: about 2 months ago - Pushed: 7 months ago - Stars: 118 - Forks: 37

akcorut/kGWASflow

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

Language: Python - Size: 610 KB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 24 - Forks: 5

roqe/PGCtest

Identifying pleiotropic genes via the composite test amidst the complexity of polygenic traits

Language: R - Size: 43 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

mattravenhall/MixedModelGWAS

Personal repository for mixed model GWAS scripts

Language: R - Size: 14.6 KB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

oncogenetics/LocusExplorer

An interactive graphical illustration of genetic associations and their biological context

Language: R - Size: 194 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 13 - Forks: 15

rivas-lab/biomarkers

Genetics of blood and urine biomarkers in the UK Biobank

Language: Jupyter Notebook - Size: 327 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 46 - Forks: 10

statmlben/nonlinear-causal

nl-causal: nonlinear causal inference based on IV regression in Python

Language: Python - Size: 35.6 MB - Last synced: 17 days ago - Pushed: 3 months ago - Stars: 12 - Forks: 0

greenelab/cimr

tool for continuously integrated meta-resource

Language: Python - Size: 34.3 MB - Last synced: 27 days ago - Pushed: about 3 years ago - Stars: 1 - Forks: 2

imyingchulo/gprs

Language: Python - Size: 556 KB - Last synced: 2 months ago - Pushed: about 1 year ago - Stars: 5 - Forks: 0

statgen/pheweb-rg-pipeline

Genetic correlation calculation pipeline via summary statistics for PheWeb

Language: Nextflow - Size: 42 KB - Last synced: 24 days ago - Pushed: about 5 years ago - Stars: 12 - Forks: 2

AdmiralenOla/Scoary

Pan-genome wide association studies

Language: Python - Size: 2.51 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 137 - Forks: 34

genepi/nf-gwas

A nextflow pipeline to perform state-of-the-art genome-wide association studies.

Language: Nextflow - Size: 65.2 MB - Last synced: 17 days ago - Pushed: about 1 month ago - Stars: 55 - Forks: 19

microbial-pangenomes-lab/panfeed

A k-mer counter that streams gene-cluster specific k-mers, while keeping k-mer positional information. Useful for microbial GWAS analyses with higher interpretability.

Language: Python - Size: 50.7 MB - Last synced: 28 days ago - Pushed: 6 months ago - Stars: 8 - Forks: 0

Speliotes-Lab/.github

About the speliotes lab

Size: 4.88 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

statgen/locuszoom-hosted

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

Language: Python - Size: 3.42 MB - Last synced: 24 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

abought/zorp

A simple GWAS parser + CLI

Language: Python - Size: 454 KB - Last synced: 28 days ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

choishingwan/PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores

Language: C - Size: 158 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 164 - Forks: 80

stephenturner/qqman

An R package for creating Q-Q and manhattan plots from GWAS results

Language: HTML - Size: 17.5 MB - Last synced: 5 days ago - Pushed: about 2 months ago - Stars: 147 - Forks: 93

roman-tremmel/ggfastman

Fast manhattenplots using ggplot2

Language: R - Size: 2.54 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 6 - Forks: 1

ladyson1806/SerohijosLab-piQTL

GitHub Repository associated with the piQTL project (Mapping effects of genome-wide genetic variation to protein-protein interactions reveals molecular mechanisms of complex traits) [ Serohijos & Michnick Lab, Université de Montréal ]

Language: Jupyter Notebook - Size: 1.72 GB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 4 - Forks: 1

AJResearchGroup/plinkr

Work with PLINK from R

Language: R - Size: 6.46 MB - Last synced: 3 months ago - Pushed: almost 2 years ago - Stars: 7 - Forks: 2

krassowski/jupyter-locuszoom

LocusZoom in Jupyter notebooks

Language: TypeScript - Size: 482 KB - Last synced: 4 days ago - Pushed: 10 months ago - Stars: 4 - Forks: 1

jinghuazhao/INF

SCALLOP-INF analysis

Language: Shell - Size: 462 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 16 - Forks: 4

RodrigoSandon/ParkisonsMicrobiomeStudy

Research under Dr. Sara Bandres-Ciga

Language: Jupyter Notebook - Size: 5.02 MB - Last synced: 3 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

nilotpalsanyal/GWASinlps

R package for Non-local Prior Based Iterative Variable Selection for Genome-Wide Association Studies, or Other High-Dimensional Data

Language: R - Size: 610 KB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

yenon118/HAPPI_GWAS_2

The HAPPI_GWAS_2 is a pipeline built for genome-wide association study (GWAS).

Language: Python - Size: 4.64 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0

OrangePomeranian/Quantitative_Genetics

Language: R - Size: 779 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

ilarsf/gwasTools

Basic and fast GWAS functions for QQ and Manhattan plots (incl. gene names)

Language: R - Size: 1.18 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 27 - Forks: 6

transbioZI/BioMM

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

Language: HTML - Size: 12.2 MB - Last synced: 17 days ago - Pushed: over 1 year ago - Stars: 14 - Forks: 1