gwas-tools

There are 3 repositories under gwas-tools topic.

statgen / locuszoom
A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.
locuszoom gwas gwas-summary-statistics gwas-tools locuszoom-plot
Language:JavaScript 157
ShujiaHuang / qmplot
A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.
visualization genomics-data-visualization matplotlib python gwas gwas-tools
Language:Python 40
akcorut / kGWASflow
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
snakemake genomics gwas gwas-pipeline kmers bioinformatics-pipeline ngs sciworkflows bioinformatics conda pipeline association-mapping bioinformatics-tool gwas-tools structural-variation workflow
Language:Python 30
RayDebashree / PLACO
A statistical test of pleiotropic effect of a genetic variant on two traits using GWAS summary statistics
pleiotropy statistical-genetics multiple-traits meta-analysis overlapping-samples gwas-summary-statistics genetic-epidemiology rscript cross-phenotype genetic-overlap gwas-tools frequentist-methods mixture-distributions
Language:R 30
BANNs
lcrawlab / BANNs
Code and simulations using biologically annotated neural networks
gwas neural-networks machine-learning interpretability genetics variable-selection bayesian-statistics gwas-tools
Language:HTML 21
katiesaund / hogwash
Three bacterial GWAS methods all rolled into one easy-to-use R package
r genomics gwas-tools gwas r-package bacterial-gwas bgwas convergence
Language:R 19
gwas-tips
esohkevin / gwas-tips
tips and tricks in genome-wide association studies - a tutorial
gwas gwas-tools gwas-pipeline gwas-dataset thesis snptest plink qctool impute2 shapeit2 admixture genotype-data chromopainter finestructure vcftools
14
genetics-statistics / faster_lmm_d
A faster lmm for GWAS. Supports GPU backend.
gpu dlang opencl arrayfire bioinformatics gwas genomics gwas-tools
Language:D 14
lorinanthony / MAPIT
Code and Tutorials for Running the MArginal ePIstasis Test (MAPIT)
epistasis epistasis-analysis linear-mixed-models variance-components heritability gwas gwas-tools gwas-case-control genetics
Language:C++ 14
BorgwardtLab / HOGImine
Higher-order genetic interaction discovery with network-based biological priors.
bioinformatics gwas-tools ismb2023 pattern-mining
Language:C++ 13
lcrawlab / i-LDSC
Code and simulations using interaction-LD score regression
epistasis gwas gwas-summary-statistics gwas-tools heritability heritability-estimation ld-score-regression
Language:Python 13
mvMAPIT
lcrawlab / mvMAPIT
The multivariate MArginal ePIstasis Test
epistasis mapit mvmapit r variance-components cpp cran epistasis-analysis gwas gwas-tools linear-mixed-models
Language:R 11
RayDebashree / GWAStools
A curated list (with links) of useful tools for genome-wide association analysis.
gwas gwas-catalog manhattan-plot qqplot genome-analysis genetic-epidemiology gwas-tools locuszoom swiss meta-analysis metal emmax skat mmlr
10
medical-genomics-group / gmrm
A Bayesian grouped mixture of regressions model capable of estimating SNP marker effect sizes for multiple outcomes simultaneously
gwas gwas-tools regression-models bayesian-statistics
Language:C++ 9
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)
gwas gwas-tools gwas-summary-statistics eqtl eqtl-mapping gtex-eqtl-association mechanism-of-action cis-regulation locuszoom phewas fine-mapping
Language:JavaScript 9
statgen / localzoom
Make interactive LocusZoom plots from a local GWAS file
locuszoom locuszoom-plot gwas gwas-tools gwas-pipeline gwas-summary-statistics gwas-catalog
Language:Vue 7
HaohanWang / CMM
Coupled Mixed Model
joint-models joint-analysis gwas gwas-tools
Language:Python 5
ramachandran-lab / ESNN
Code and simulations using an Ensemble of Single-Effect Neural Networks (ESNN)
machine-learning gwas genetics variable-selection neural-networks bayesian-statistics interpretability gwas-tools
Language:Python 5
snaketron / genphen
Tool for genome wide association studies with Bayesian inference and statistical learning
gwas gwas-pipeline gwas-tools bayesian-inference snp genotype-phenotype-map random-forest machine-learning bioinformatics
Language:R 5
Snitkin-Lab-Umich / prewas
R package to perform data pre-processing for more informative bacterial GWAS
r-package r microbiology gwas gwas-tools bacterial-genomes
Language:R 5
regens
EpistasisLab / regens
Recombines real genomic segments to simulate whole genomes
simulated-datasets gwas-tools
Language:Python 4
matthijsknigge / mendelianrandomization
MendelianRandomization is an R package for assessing causal relationships using genetic variants as instrumental variables
data-science genetics gwas-tools mendelian-randomisation mr-egger pascal r pathway-scoring-algorithm wald-ratio inverse-variance-weighted-method
Language:R 4
RayDebashree / mvtests
mvtests: a suite of functions for testing genetic associations of multiple traits (a.k.a. cross-phenotype associations)
cross-phenotype multiple-traits proportional-odds-regression gwas gwas-tools genome-analysis statistical-genetics statistical-tests genetic-epidemiology multivariate-analysis
Language:R 4
sinarueeger / ggGWAS
R package 📦 with ggplot2 extensions for GWAS summary statistics (still in 🚧)
ggplot2-geom gwas-tools gwas r r-package rstats
Language:HTML 4
GreallyLab / gaiaAssociation
gaiaAssociation is a tool to detect the cell specific enrichment of loci in regulatory regions through the sum of non-identical binomials
enrichment genetics gwas-tools next-generation-sequencing open-chromatin-regions
Language:Python 3
jennasimit / flashfm
Flashfm: multi-trait fine-mapping that uses GWAS summary statistics from several traits. Updated and more flexible wrapper functions available at jennasimit.github.io/flashfmZero/
fine-mapping gwas-tools multi-trait gwas
Language:R 3
jennasimit / MGflashfm
MGflashfm: joint fine-mapping of genetic association signals in several traits amongst multiple population groups.
fine-mapping gwas-tools multi-trait gwas multi-ancestry
Language:R 3
npredey / GeneticAncestryTool
bioinformatics-tool gwas-tools hapmap pca plink principal-component-analysis
Language:Python 3
UVIC_TFM_AGomez_2023
antoniogomez / UVIC_TFM_AGomez_2023
Scripts of Final Master Project
eqtl gwas-tools mirna-seq qtl qtl-analyses qtl-mapping
Language:R 1
hagax8 / PathAnalyzor
Just another wrapper for pathway analysis using MAGMA
gwas-tools pathway-analysis pathway-enrichment-analysis
Language:Shell 1
luisgarreta / multiGWAS
MultiGWAS tool for Genome-Wide Association Studies (GWAS) in plants (diploide and tetraploide)
r gwas-tools bioinformatics
Language:HTML 1
MCBRLab / ISR_GWAS
Mult-Loci nonlinear/Linear Model based on new algorithm For GWAS , Epistasis and GS（ISR）
gwas gwas-tools isr
Language:MATLAB 1
RayDebashree / TDT-like-tests
Modified transmission disequilibrium test (TDT) for GWAS using case-parent/control-parent trios.
gwas-tools family-data trio transmission-disequilibrium tdt case-parent-control-parent family-based-design nuclear-family
Language:R 1
statgen / locuszoom-hosted
A web service to upload and share GWAS results with LocusZoom.js
locuszoom locuszoom-plot gwas gwas-summary-statistics gwas-pipeline gwas-tools
Language:Python 1
statgen / zorp
A simple GWAS parser + CLI
gwas-summary-statistics gwas-tools gwas-pipeline gwas parsers conversion python locuszoom
Language:Python 1
Zepeng-Mu / qqman
This is a fork from qqman package
gwas gwas-tools manhattan-plot qtl-analyses qtl colocalization
Language:R 1