Data visualization software tools | Genome-wide association study data 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.
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 association signal relative to genomic position, local linkage disequilibrium (LD) and recombination patterns and the positions of genes in the region.
Aims to visualize genome-wide association studies (GWAS) results using quantile-quantile (Q-Q) and manhattan plots. Qqman enables the flexible creation of manhattan plots, both genome-wide and for single chromosomes, with optional highlighting of single nucleotide polymorphisms (SNPs) of interest. It can be easily integrated into existing workflows to further enable automated reproducible research.
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 connects to the latest online genomic databases to annotate the SNPs and their associated P-values in the context of predicted gene structure and SNP function, association with gene expression, evidence of recent selection, and concurrent evidence from multiple association studies.
Displays regions of interest in select genome wide association study (GWAS) data sets. Ricopili colors independent regions in different color, highlighting linkage disequilibrium (LD). It employs HapMap to anonymize data.
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. FlashPCA enables scalable and accurate PCA of large genotype datasets, using small amounts of memory, making it feasible to run such analyses on a standard personal computer, all within the R environment.
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 plots for particular markers or viewing a set of single nucleotide polymorphisms (SNPs) showing evidence for association. The software also allows users to visualize the effect triggers by excluding specific samples, and view multiple collections side by side to compare genotype calls across sample sets.
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 or analysis, as well as related information such as genetic effect size and summary phenotype information, are available for plotting according to user preference.