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Search results for gwas
gwas
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114 search results found
Hail
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905
Cloud-native genomic dataframes and batch computing
Glow
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251
An open-source toolkit for large-scale genomic analysis
Sgkit
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194
Statistical genetics toolkit
Gwa_tutorial
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184
A comprehensive tutorial about GWAS and PRS
Prsice
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151
A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
Qqman
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141
An R package for creating Q-Q and manhattan plots from GWAS results
Locuszoom
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132
A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.
Gwas_scripts
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127
Codebook from my GWAS cookbook
Variantspark
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121
machine learning for genomic variants
Mtag
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118
Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
Ldblockshow
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102
LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
Rvtests
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95
Rare variant test software for next generation sequencing data
Pyseer
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81
SEER, reimplemented in python 🐍🔮
Tiledb Vcf
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79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Scdrs
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75
Single-cell disease relevance score (scDRS)
Scoary
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71
Pan-genome wide association studies
Polyfun
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69
PolyFun (POLYgenic FUNctionally-informed fine-mapping)
Ukb_rap
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68
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.
Geneticsmakie.jl
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66
🧬High-performance genetics- and genomics-related data visualization using Makie.jl
Imputationserver
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66
Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity
Vcf2gwas
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62
Python API for comprehensive GWAS analysis using GEMMA
Mungesumstats
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59
Rapid standardisation and quality control of GWAS or QTL summary statistics
Nf Gwas
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52
A nextflow pipeline to perform state-of-the-art genome-wide association studies.
Magma_celltyping
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50
Find causal cell-types underlying complex trait genetics
Gwastutorial
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45
GWAS Tutorial for Beginners
Locuscomparer
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42
LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.
Gwas2vcf
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41
Convert GWAS summary statistics to VCF
Mixer
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41
Causal Mixture Model for GWAS summary statistics
Gor
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37
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.
Seer
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35
sequence element (kmer) enrichment analysis
Bgwas
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33
R package to perform Bayesian Genome-Wide Association Studies
Lme4qtl
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33
Mixed models @lme4 + custom covariances + parameter constraints
Bgdata
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30
A Suite of Packages for Analysis of Big Genomic Data
Qmplot
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29
A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.
Qtcat
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25
Quantitative Trait Cluster Association Test in R
Snpsea
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23
📊 Identify cell types and pathways affected by genetic risk loci.
Hierfstat
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22
the hierfstat package
Genamap
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22
Visual Machine Learning of Genome-Phenome Associations
Mendeliht.jl
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21
Iterative hard thresholding for l0 penalized regression
Echolocator
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20
Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.
Sumstatsrehab
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20
GWAS summary statistics files QC tool
Candihap
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20
A haplotype analysis toolkit for natural variation study.
Gwas Pipeline
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20
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.
Kgwasflow
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19
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
Twas_sim
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19
Using real genotype data, simulate a complex trait as a function of latent expression, fit eQTL weights in independent data, and perform GWAS/TWAS on complex trait.
Ordinalgwas.jl
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18
Genome-wide association studies (GWAS) for ordered categorical phenotypes
Gchromvar
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18
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
Permgwas
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17
Efficient Permutation-based GWAS for Normal and Skewed Phenotypic Distributions
Rtassel
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17
R front-end for TASSEL
Adjclust
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16
Adjacency-constrained hierarchical clustering of a similarity matrix
Gglocuszoom
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15
Create LocusZoom-style plots in R.
Farmcpupp
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14
Perform GWAS using the FarmCPU model.
Hase
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14
Framework for efficient high-dimensional association analyses.
S Pcgc
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14
Heritability, genetic correlation and functional enrichment estimation for case-control studies
Haptools
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13
Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis
Containers
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13
CoMorMent-Containers
Gentropy
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13
Open Targets python framework for post-GWAS analysis
Gwastools
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13
Basic and fast GWAS functions for QQ and Manhattan plots (incl. gene names)
Gwas
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12
UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies
Dak
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12
Explaining the genetic causality for complex diseases by deep association kernel learning
Faster_lmm_d
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12
A faster lmm for GWAS. Supports GPU backend.
Gwastoolkit
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12
A collection of scripts to run GWAS, regional, gene-oriented, or per-variant analyses.
Cataloguer
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12
Easy-to-use R wrappers for the eQTL Catalogue's API (both with tabix and the REST API).
Npdr
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12
NPDR: Nearest-neighbor Projected-Distance Regression with the generalized linear model
Genepi
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11
A package for detecting epistasis by machine learning
Introduction_to_gwas
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11
https://filippob.github.io/introduction_to_gwas/
Pygwas
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11
Biomarkers
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11
Genetics of blood and urine biomarkers in the UK Biobank
Sushie
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11
Software to perform multi-ancestry SNP fine-mapping on molecular data
Knockoffgwas
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11
A flexible tool for the multi-resolution localization of causal variants across the genome, accounting for population structure.
Metausat
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10
metaUSAT is a data-adaptive statistical approach for testing genetic associations of multiple traits from single/multiple studies using univariate GWAS summary statistics.
Mklmm
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10
Multi Kernel Linear Mixed Models for Complex Phenotype Prediction
Gwaspy
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10
GWAS QC, PCA, haplotype phasing, genotype imputation
Mendelplots.jl
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10
Julia package for plotting results from GWAS
Banns
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10
Code and simulations using Biologically Annotated Neural Networks (BANNs)
Nonlinear Causal
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10
nl-causal: nonlinear causal inference based on IV regression in Python
Sumstats
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10
Format of GWAS summary statistics.
Metagwastoolkit
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10
A ToolKit to perform a Meta-analysis of Genome-Wide Association Studies
Glow Solution Accelerator
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10
Genome-wide association studies identify genetic variations associated with a target disease or trait. Researchers and clinicians can use this information to better detect, treat and prevent chronic health conditions. This Solution Accelerator notebook builds on top of Glow
Hogwash
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10
Three bacterial GWAS methods all rolled into one easy-to-use R package
Gwas Tips
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9
tips and tricks in genome-wide association studies - a tutorial
Gimpute
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9
An efficient genetic data imputation pipeline
Mapit
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9
Code and Tutorials for Running the MArginal ePIstasis Test (MAPIT)
Gwas Vcf Specification
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9
Specification for the GWAS-VCF format (manuscript in preparation)
Rhoge
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9
Estimate genetic correlation using predicted expression
Bcfr
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9
Bin-map Constructer For RILs
Biomm
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9
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
Mvmapit
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8
The multivariate MArginal ePIstasis Test
Bakr
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8
Code and Simulations using Bayesian Approximate Kernel Regression (BAKR)
Multiskat
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8
MultiSKAT is an R-package focused at rare-variant analysis of continuous multiple phenotype data. This project contains the R-codes/functions (including an example dataset) to carry out the MultiSKAT tests.
Saigegds
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8
Scalable Implementation of generalized mixed models using GDS files in Phenome-Wide Association Studies
Statgengwas
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8
See https://biometris.github.io/statgenGWAS for a full description
Quincunx
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8
quincunx: an R package to query, download and wrangle PGS Catalog data
Locusexplorer
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8
An interactive graphical illustration of genetic associations and their biological context
Ipat
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7
iPat allows you to perform GWAS and GS with drags and clicks!
Mr_bacon
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7
Mendelian Randomization with Biomarker Associations for Causality with Outcomes
S Ldxr
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7
Stratified squared trans-ethnic genetic correlation
Inf
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7
SCALLOP-INF analysis
Tad_pathways_pipeline
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7
Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs
Emmax Pipeline
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6
GWAS analysis process based on EMMAX software
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