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Multivariate analysis software tools | Genome-wide association study

Joint association analysis of multiple traits in a genome-wide association study offers several advantages over analyzing each trait in a separate GWAS. Several methods that have been developed to perform multiple trait analysis.

PLINK
Desktop

PLINK

A free, open-source whole genome association analysis toolset, designed to…

A free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on…

SNPTEST
Desktop

SNPTEST

A program for the analysis of single SNP association in genome-wide studies.…

A program for the analysis of single SNP association in genome-wide studies. The tests implemented include 1) binary (case-control) phenotypes, single and multiple quantitative phenotypes, 2)…

CPASSOC
Desktop

CPASSOC

Integrates association evidence from multiple correlated continuous and binary…

Integrates association evidence from multiple correlated continuous and binary traits from one or multiple studies. CPASSOC is a general approach that proposes general statistics allowing to detect…

GSU
Desktop

GSU Generalized Similarity U

Tests the association between complex objects. The theoretical properties of…

Tests the association between complex objects. The theoretical properties of GSU was studied in a general setting and then focused on the application of the test to sequencing association studies.…

TreeQTL
Desktop

TreeQTL

Implements a hierarchical multiple testing procedure. In the context of eQTL…

Implements a hierarchical multiple testing procedure. In the context of eQTL studies, TreeQTL provides methods allowing control of the false discovery rate or family wise error rate for the discovery…

hierGWAS
Desktop

hierGWAS

A method for assigning statistical significance in GWAS. We propose a procedure…

A method for assigning statistical significance in GWAS. We propose a procedure in which all the SNPs are analyzed in a multiple generalized linear model, and we show its use for extremely…

GATE
Desktop

GATE Group Accumulated Test Evidence

Allows association studies between multiple traits and a unique single…

Allows association studies between multiple traits and a unique single nucleotide polymorphism (SNP). GATE performs the principal component analysis (PCA) on all traits and calculates the p-values of…

LLR
Desktop

LLR Latent Low-Rank

Colocalizes genetic risk variants through the analysis of summary statistics,…

Colocalizes genetic risk variants through the analysis of summary statistics, specifically Z-scores. LLR is a statistical approach to prioritizing risk variants using the pleiotropy across multiple…

MGAS
Desktop

MGAS Multivariate Gene-based Association test by extended Simes procedure

A method that allows gene-based testing of multivariate phenotypes in unrelated…

A method that allows gene-based testing of multivariate phenotypes in unrelated individuals. MGAS allows researchers to conduct their multivariate gene-based analyses efficiently, and without the…

An efficient…
Algorithm
OPTPDT
Desktop

OPTPDT Optimal P-value Threshold Pedigree Disequilibrium Test

A multi-SNP association test using a variable p-value threshold algorithm to…

A multi-SNP association test using a variable p-value threshold algorithm to select SNPs with the strongest association signal at a particular p-value threshold. The OPTPDT will be helpful for…

MultiPhen
Desktop

MultiPhen

A package for the genetic association testing of multiple phenotypes. MultiPhen…

A package for the genetic association testing of multiple phenotypes. MultiPhen performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).

BALD
Desktop

BALD Blockwise Approach using Linkage Disequilibrium

A three-step approach that takes into account the biological information of the…

A three-step approach that takes into account the biological information of the linkage disequilibrium between variables by firstly inferring LD blocks, then estimating the number of such blocks, and…

TATES
Desktop

TATES Trait-based Association Test that uses Extended Simes procedure

A software tool for multivariate GWAS based on P-values from GWAS. For each…

A software tool for multivariate GWAS based on P-values from GWAS. For each component of a multivariate trait, TATES combines p-values obtained in standard univariate GWAS to acquire one trait-based…

GFlasso
Desktop

GFlasso Graph-guided Fused lasso

A program for association analysis that searches for genetic variations…

A program for association analysis that searches for genetic variations influencing a group of correlated traits. This approach represents the dependency structure among the quantitative traits…

PRIMe
Desktop

PRIMe Pleiotropic Region Identification Method

A software tool to systematically identify and characterize genomic regions…

A software tool to systematically identify and characterize genomic regions where low association P-values are observed with multiple traits. PRIMe can be downloaded and run on local machines without…

PCHAT
Desktop

PCHAT Principal Component of Heritability Association Test

A method of iterated sample splitting that uses one portion of the data for…

A method of iterated sample splitting that uses one portion of the data for training and the remainder for testing. This cross-validation approach maintains the type I error control and yet utilizes…

lavaan
Desktop

lavaan

Package to estimate a large variety of multivariate statistical models,…

Package to estimate a large variety of multivariate statistical models, including path analysis, confirmatory factor analysis, structural equation modeling and growth curve models.

JAMP
Desktop

JAMP

Uses raw data as input and evaluates the multivariate evidence for association…

Uses raw data as input and evaluates the multivariate evidence for association of multiple phenotypes for a SNP. JAMP also provides a family-wise corrected P-value.

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