gwas

There are 18 repositories under gwas topic.

• hail

  hail-is / hail

  Cloud-native genomic dataframes and batch computing

  geneticsvcfgenomicsgwasbioinformaticspythonsoftwarehail
  Language:Python 956

• MareesAT / GWA_tutorial

  A comprehensive tutorial about GWAS and PRS

  bioinformaticsgeneticsgenomicsgwasplinkpopulation-stratificationpopulation-structureprsqcrunix
  792

• projectglow / glow

  An open-source toolkit for large-scale genomic analysis

  deltagenomicsgwasmachine-learningpopulation-geneticsregressionspark
  Language:Scala 262

• sgkit-dev / sgkit

  Scalable genetics toolkit

  geneticsgwaspopgenpydatastatgenstatistical-genetics
  Language:Python 220

• JoniColeman / gwas_scripts

  Codebook from my GWAS cookbook

  gwasimputationquality-control
  Language:R 181

• choishingwan / PRSice

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

  gwasprs
  Language:C 175

• JonJala / mtag

  Python command line tool for Multi-Trait Analysis of GWAS (MTAG)

  gwasmtagmulti-trait-analysisstatistical-genetics
  Language:Python 164

• stephenturner / qqman

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

  genomicsrgwascran
  Language:HTML 151

• statgen / locuszoom

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

  gwasgwas-summary-statisticsgwas-toolslocuszoomlocuszoom-plot
  Language:JavaScript 149

• AdmiralenOla / Scoary

  Pan-genome wide association studies

  bacteriagene-presence-absencegenomicsgwaspan-genome
  Language:Python 145
• VariantSpark

  aehrc / VariantSpark

  machine learning for genomic variants

  variant-sparkgwasrandom-forestgenomeassociation-studiesvcfvariantsparknotebookdatabricksbioinformaticsawsemr
  Language:JavaScript 138

• BGI-shenzhen / LDBlockShow

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

  ld-heatmapgwasld-blockldlinkage-disequilibria
  Language:Perl 130

• zhanxw / rvtests

  Rare variant test software for next generation sequencing data

  next-generation-sequencingngsassociation-analysisgwasrare-variantmeta-analysisgenotypeskatc-plus-plusvariantsumichgeneticskernelvcf-files
  Language:C++ 126

• Cloufield / GWASTutorial

  GWAS Tutorial for Beginners

  gwas
  Language:Jupyter Notebook 118

• 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.

  ukbiobankwdlgwas
  Language:Jupyter Notebook 106

• mgalardini / pyseer

  SEER, reimplemented in python 🐍🔮

  bacteriagwask-merreimplementationreproducible-science
  Language:Python 106

• martinjzhang / scDRS

  Single-cell disease relevance score (scDRS)

  cell-stategwassingle-cell-rna-seqdiseases-and-complex-traitswithin-cell-type-heterogeneity
  Language:Jupyter Notebook 96

• boxiangliu / locuscomparer

  LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.

  colocalizationeqtlgwas
  Language:R 95

• frankvogt / vcf2gwas

  Python API for comprehensive GWAS analysis using GEMMA

  gwasvcfgemma-analysis
  Language:Python 83
• polyfun

  omerwe / polyfun

  PolyFun (POLYgenic FUNctionally-informed fine-mapping)

  statistical-geneticsgwasfine-mapping
  Language:Python 83

• TileDB-Inc / TileDB-VCF

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

  bioinformaticsdata-sciencegenomicsgwaspythonsparktiledbvariant-callingvcf
  Language:C++ 83

• mmkim1210 / GeneticsMakie.jl

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

  geneticsgenomicsjuliavisualizationmakiebioinformaticscairomakiegwasphewaslocuszoomcolocalizationfine-mappingqtllinkagejulia-languagedata-sciencemulti-ethnicv2fmultivariateopenmendel
  Language:Julia 76

• 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

  imputationgwassoftware-as-a-serviceminimac4
  Language:Java 73

• neurogenomics / MungeSumstats

  Rapid standardisation and quality control of GWAS or QTL summary statistics

  bioinformaticsrgwassummary-statisticsbioconductor-packager-packagestandardisationgenomicsvcf-filesdatabase-apiqtl
  Language:R 71
• MAGMA_Celltyping

  neurogenomics / MAGMA_Celltyping

  Find causal cell-types underlying complex trait genetics

  gwasgenomicssingle-cell-omicsmagmasingle-cellsnpsstatistical-genetics
  Language:R 68

• genepi / nf-gwas

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

  gwasimputationnextflowregeniesingularityslurm
  Language:Nextflow 61

• precimed / mixer

  Causal Mixture Model for GWAS summary statistics

  gwaspopulation-geneticslinkage-disequilibriumsummary-statistics
  Language:C 53

• variani / lme4qtl

  Mixed models @lme4 + custom covariances + parameter constraints

  lme4qtlcovariancegwaskinshipibdpedigreerelatednessfamilyvariance-covariancerandom-effects
  Language:R 48

• MRCIEU / gwas2vcf

  Convert GWAS summary statistics to VCF

  gwasbioinformaticsvcfconvertersummary-statistics
  Language:Python 43

• caleblareau / gchromVAR

  Cell type specific enrichments using finemapped variants and quantitative epigenetic data

  gwasepigeneticsatac-seqsingle-cell
  Language:R 42

• johnlees / seer

  sequence element (kmer) enrichment analysis

  gwasbacteriak-mer
  Language:C++ 42

• 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.

  geneticsgenomicsgwasbioinformaticspythonsoftwaregorgorpipevcfsparkopen-sourcescalajava
  Language:Java 39

• neurogenetics / GWAS-pipeline

  This is a general (somewhat comprehensive) description of the LNG GWAS pipeline which can be used to guide researchers on how-to run a GWAS.

  gwas-pipelinegwas
  Language:R 39

• n-mounier / bGWAS

  R package to perform Bayesian Genome-Wide Association Studies

  bayesiangwasr-packagestatistical-genetics
  Language:R 37

• ShujiaHuang / qmplot

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

  visualizationgenomics-data-visualizationmatplotlibpythongwasgwas-tools
  Language:Python 35

• slowkow / snpsea

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

  risk-locigenetissuegene-setsalgorithmenrichmentgwasbioinformatics
  Language:C++ 35