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Data visualization software tools | Genome-wide association analysis

Genome-wide association studies (GWAS) are an important tool for the mapping of complex traits and diseases. Visual inspection of genomic annotations may be used to generate insights into the biological mechanisms underlying GWAS-identified loci.…
DANCE
Web

DANCE Disease-ANCEstry Networks

A graph-based web tool that allows to integrate and visualize information on…

A graph-based web tool that allows to integrate and visualize information on human complex phenotypes and their GWAS-hits, as well as their risk allele frequencies in different populations. DANCE…

WGAViewer
Desktop

WGAViewer

A suite of JAVA software tools that provides a user-friendly interface to…

A suite of JAVA software tools that provides a user-friendly interface to annotate, visualize, and help interpret the set of P-values emerging from a whole genome association (WGA) study. WGAViewer…

graph-GPA
Desktop

graph-GPA

Identifies risk variants for complex traits through a joint analysis of…

Identifies risk variants for complex traits through a joint analysis of multiple Genome-Wide Association Studies (GWAS) datasets by leveraging pleiotropy. graph-GPA integrates a large number of GWAS…

Evoker
Desktop

Evoker

Visualizes genotype cluster plots designed to be integrated into quality…

Visualizes genotype cluster plots designed to be integrated into quality control workflows for Genome-wide association studies (GWAS). Evoker provides a wide range of functionalities such as calling…

FlashPCA
Desktop

FlashPCA Flash principal component analysis

Performs Principal Component Analysis (PCA) on 1 million individuals faster…

Performs Principal Component Analysis (PCA) on 1 million individuals faster than competing approaches. FlashPCA uses bounded memory and maintains high accuracy for the top eigenvalues/eigenvectors.…

GWASrap
Web

GWASrap

A tool that systematically supports genetic variant representation, annotation…

A tool that systematically supports genetic variant representation, annotation and prioritization for data generated from GWAS and NGS. GWASrap utilizes state-of-the-art web technologies to maximize…

Assocplots
Desktop

Assocplots

A python package for viewing and exploring GWAS results not only using classic…

A python package for viewing and exploring GWAS results not only using classic static Manhattan and quantile-quantile plots, but also through a dynamic extension which allows to visualize data…

Zbrowse
Desktop

Zbrowse

An interactive GWAS viewer focused on comparing results across traits and other…

An interactive GWAS viewer focused on comparing results across traits and other variables. Zbrowse can easily be run on a desktop computer with software that bioinformaticians are likely already…

EnigmaVis
Web

EnigmaVis

Provides a straightforward way to visually examine the large quantities of data…

Provides a straightforward way to visually examine the large quantities of data collected through the Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) consortium. EnigmaVis is an…

RadialMR
Desktop

RadialMR

Allows user to reproduce radial plots. RadialMR also performs radial regression…

Allows user to reproduce radial plots. RadialMR also performs radial regression for the mendelian randomization (MR)-setting.

qqman
Desktop

qqman

A R package for visualizing GWAS results using Q-Q and manhattan plots. The…

A R package for visualizing GWAS results using Q-Q and manhattan plots. The qqman package enables the flexible creation of manhattan plots, both genome-wide and for single chromosomes, with optional…

AssociationView…
Desktop

AssociationViewer

Allows visualization of large-scale genetic and genomic data exemplified by…

Allows visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies (GWAS). AssociationViewer provides an integrated framework to facilitate the…

cgmisc
Desktop

cgmisc

An R package that enables enhanced data analysis and visualisation of results…

An R package that enables enhanced data analysis and visualisation of results from GWAS. The package contains several utilities and modules that complement and enhance the functionality of the…

Synthesis-View
Web
Desktop

Synthesis-View

A software to visualize genotype-phenotype association data in multiple…

A software to visualize genotype-phenotype association data in multiple cohorts. Through the use of stacked data-tracks, information on SNP genomic locations, presence of the SNP in a specific study…

GenAMap
Desktop

GenAMap

An interactive analytics software platform that 1) automates the execution of…

An interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression…

gwascat
Desktop

gwascat

Uses GRanges and allied infrastructure allowing users to ease visualization of…

Uses GRanges and allied infrastructure allowing users to ease visualization of data from the European Bioinformatics Institute Main Building (EMBL-EBI) genome-wide association study (GWAS) catalog.

LocusTrack
Web

LocusTrack

A web-based application that annotates and creates plots of regional GWAS…

A web-based application that annotates and creates plots of regional GWAS results and incorporates user-specified tracks that display annotations such as linkage disequilibrium (LD), phylogenetic…

LocusZoom
Desktop

LocusZoom

A tool to plot regional association results from genome-wide association scans…

A tool to plot regional association results from genome-wide association scans or candidate gene studies. LocusZoom visually displays regional information such as the strength and extent of the…

GWAS GUI
Desktop

GWAS GUI

An interactive package that provides graphical overviews of the results of…

An interactive package that provides graphical overviews of the results of whole-genome association studies in datasets with rich multi-dimensional phenotypic information, such as global surveys of…

EINVis
Web

EINVis

A visualization tool that is specifically designed to analyze and explore…

A visualization tool that is specifically designed to analyze and explore genetic interactions. EINVis displays interactions among genetic markers as a network. EINVis utilizes a circular layout…

SNPEVG
Desktop

SNPEVG

A set of graphical tools for instant global and local viewing and graphing of…

A set of graphical tools for instant global and local viewing and graphing of GWAS results for all chromosomes and for each trait. The SNPEVG package is a versatile, flexible and efficient graphical…

LDassoc
Web

LDassoc

Allows exploration of genome-wide association studies (GWAS) association…

Allows exploration of genome-wide association studies (GWAS) association results. LDassoc is a web module, in the LDlink suite of web tools, allowing users to upload and visualize GWAS association…

Goldsurfer
Desktop

Goldsurfer

Allows users to proceed genome wide association studies (GWAS). Goldsurfer is a…

Allows users to proceed genome wide association studies (GWAS). Goldsurfer is a standalone software that can be used for managing a complete GWA project. It is able to analyze results from publicly…

LocusExplorer
Desktop
Web

LocusExplorer

A data visualisation and exploration tool for genetic association data.…

A data visualisation and exploration tool for genetic association data. LocusExplorer is written in R using the Shiny library, providing access to powerful R-based functions through a simple user…

MAVEN
Web

MAVEN Management, Analysis, Visualization and rEsults sharing

Allows users to visualize Genome-wide association studies (GWAS) results. MAVEN…

Allows users to visualize Genome-wide association studies (GWAS) results. MAVEN provides four main functionalities: (i) it accepts and stores GWAS results based on single-locus analysis methods, not…

LD-Plus
Web

LD-Plus

A data visualization application for the display of single SNP statistics in…

A data visualization application for the display of single SNP statistics in the context of linkage disequilibrium and haplotype structures. LD-Plus can display both continuous and categorical SNP…

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