HelixTree
HelixTree is the leading software application for population-based candidate gene and genome-wide association studies. Its unique set of conventional and leading-edge analysis tools enable you to uncover more novel associations than any other program.
Data Management
The core architecture of HelixTree has been completely reinvented to efficiently handle datasets of virtually any size and type on a desktop computer. Supported dependent variables include case-control and quantitative traits. Predictors can be binary, continuous, ordinal, categorical, nominal, and genetic (bi- and multi-allelic SNPs, log ratios, CNVs, microsatellites, etc.). Learn more
Quality Assurance
High quality data is key to quality results. Considerable effort has been made to enhance quality assurance at every step. You can now easily generate a number of genotype statistics, view cluster plots of allele intensities, check gender and marker concordance, perform variance analysis on log ratios, filter poor quality markers and samples, and more. Further, HelixTree offers a powerful principal component analysis (PCA) approach for both SNP and CNV data to simultaneously correct for batch effects, genomic waves, and population stratification.
Learn more
Richly Interactive Data Visualization
A new dynamic analytic visualization tool with integrated genome browser offers exceptional flexibility in how you visualize data and represent results. Gain greater insights with unprecedented whole genome views and navigation control. Apply data transformations or analytic functions in real-time and save plots to a number of publication quality formats, including scalable vector graphics. Learn more
Spreadsheet Manipulation, Editing and Data Enrichment
HelixTree offers real-time spreadsheet manipulation, data editing, and enrichment helping to eliminate the hassles of working with large-scale, complex data. Easily combine multiple sample sets and data of different types, from different arrays, or even platforms. Quickly recode genotypes based on a specified genetic model, flip DNA strands, transcode from AB to AGCT formats, and more. Further, an integrated spreadsheet editor facilitates data editing and transformations on a grand scale. Learn more
Genetic Association Testing
HelixTree delivers the most extensive array of genetic association tests including allele, genotype, haplotype, CNV, ROH, LD, and advanced linear and logistic regression. Within a streamlined interface test against either cases vs. controls or quantitative traits using a variety of statistical measures under any one of several genetic model assumptions. Tests can be run individually or simultaneously while also correcting for stratification and applying a number of multiple testing corrections, including permutation testing.
Learn more
Fully Programmatic Scripting and Automation
Automate workflows, incorporate custom methods, or interoperate with other programs. These are just a few examples of how you can enhance the utility of HelixTree and other SVS 7 modules with a fully programmatic Python scripting interface. HelixTree now includes an integrated Python editor that makes it easy to read and write scripts helping even novice users realize the power of scripting. Learn more