Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Complex trait prediction software tools | Genome-wide association analysis

The success of genome-wide association studies (GWASs) has led to increasing interest in making predictions of complex trait phenotypes, including disease, from genotype data. Rigorous assessment of the value of predictors is crucial before…
SMR
Desktop

SMR Summary-data-based Mendelian Randomization

Identifies associations between gene expression and complex traits using…

Identifies associations between gene expression and complex traits using summary data from genome-wide association studies (GWAS) and expression quantitative trait locus (eQTL). Then, a heterogeneity…

GREML-LDMS
Desktop

GREML-LDMS

Estimates heritability using whole genome sequence data. GREML-LDMS can be…

Estimates heritability using whole genome sequence data. GREML-LDMS can be applied to genome-wide association studies (GWAS) data with hundreds of human complex traits and diseases. From simulations…

BOLT-REML
Desktop

BOLT-REML

Employs the conjugate gradient-based iterative framework for mixed model…

Employs the conjugate gradient-based iterative framework for mixed model computations. BOLT-REML estimates variance parameters for models involving multiple variance components and multiple traits.…

MTG
Desktop
GraBLD
Desktop

GraBLD Gradient boosted and LD adjusted

Predicts polygenic traits. GraBLD is a heuristic based on machine-learning…

Predicts polygenic traits. GraBLD is a heuristic based on machine-learning concepts to improve the prediction of polygenic traits using gene scores. The software involves two steps and uses the…

TPIEA
Desktop

TPIEA Tissue-specific Pathway Interaction Enrichment Analysis

Summaries and identifies several pathways for bone mineral density. This…

Summaries and identifies several pathways for bone mineral density. This GWAS-based pathway analysis approach may help to fill the gap of classic pathway association analysis approaches by…

iCTNet
Desktop

iCTNet integrated Complex Traits Network

Allows automated and systematic creation of networks. iCTNet facilitates the…

Allows automated and systematic creation of networks. iCTNet facilitates the generation of general or specific network views with diverse options for more than 200 diseases. It provides omics…

RicePPINet
Dataset

RicePPINet

Provides an expanded landscape of computational interactome for genetic…

Provides an expanded landscape of computational interactome for genetic dissection of agronomically important traits in rice. RicePPINet is a genome-wide rice protein-protein interaction (PPI)…

GoShifter
Desktop

GoShifter Genomic Annotation Shifter

A statistical approach to assess whether enriched annotations are able to…

A statistical approach to assess whether enriched annotations are able to prioritize causal variation. GoShifter employs an intuitive method that locally shifts sites of tested features within each…

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…

MEGHA
Desktop

MEGHA Massively Expedited Genome-wide Heritability Analysis

Allows for examination of complex phenotypes and the development of…

Allows for examination of complex phenotypes and the development of nonparametric sampling techniques. MEGHA is a statistical method for large-scale heritability analysis using genome-wide…

HERRA
Desktop

HERRA Heritability Estimation using a Regularized Regression Approach

Provides a simple, efficient and consistent estimators of the narrow-sense…

Provides a simple, efficient and consistent estimators of the narrow-sense heritability based on Genome Wide Association Study (GWAS) data. HERRA is a heritability estimation approach using…

OmicKriging
Desktop

OmicKriging

Predicts complex traits. OmicKriging leverages and integrates similarity in…

Predicts complex traits. OmicKriging leverages and integrates similarity in genetic, transcriptomic, and/or other large scale omics data. It emphasizes the use of a wide variety of systems-level…

GetSynth
Desktop

GetSynth

Methods implemented in the software tool GetSynth for the search for…

Methods implemented in the software tool GetSynth for the search for multi-locus haplotype markers in near perfect linkage disequilibrium (LD) with a genome-wide association studies (GWAS) tag…

TV-GroupSpAM
Desktop

TV-GroupSpAM Time-Varying Group Sparse Additive Models

A method for association mapping that considers dynamic phenotypes measured at…

A method for association mapping that considers dynamic phenotypes measured at a sequence of time points. TV-GroupSpAM relies on the use of time-varying group sparse additive models for…

uFineMap/uHDSet
Desktop

uFineMap/uHDSet

A unified marker wise test (uFineMap) to accurately localize causal loci and a…

A unified marker wise test (uFineMap) to accurately localize causal loci and a unified high-dimensional set based test (uHDSet) to identify high-dimensional sparse associations in deep sequencing…

MultiBLUP
Desktop

MultiBLUP

Extends the BLUP (best linear unbiased prediction) model to include multiple…

Extends the BLUP (best linear unbiased prediction) model to include multiple random effects, allowing greatly improved prediction when the random effects correspond to classes of SNPs with distinct…

PoCos
Desktop

PoCos Population Covering locus sets

Identifies the multiple functionally related genomic variants that are…

Identifies the multiple functionally related genomic variants that are collectively associated with a phenotype. PoCos allows to users to assess the collective disease-association of multiple genomic…

PRSoS
Desktop

PRSoS PRS-on-Spark

Allows users to measure polygenic risk scores (PRS). PRSoS provides enhanced…

Allows users to measure polygenic risk scores (PRS). PRSoS provides enhanced data output options and can be applied to observed genotypes, hard calls, and imputed posterior probabilities. It also…

AnnoPred
Desktop

AnnoPred

Improves risk prediction accuracy. AnnoPred integrates Genome-Wide Association…

Improves risk prediction accuracy. AnnoPred integrates Genome-Wide Association Studies (GWAS) summary statistics with various types of annotation data. It uses simulations and real data of multiple…

REALbreeding
Desktop

REALbreeding

Predicts untested single crosses (SCs) in plant breeding. REALbreeding aims to…

Predicts untested single crosses (SCs) in plant breeding. REALbreeding aims to assess the prediction efficiency by correlating the predicted and true genotypic values of untested SCs. It uses…

P2BAT
Desktop

P2BAT

Provides a massive parallel and user friendly implementation of the…

Provides a massive parallel and user friendly implementation of the PBAT-analysis tools for family based association tests (FBATs) in large-scale studies, including genome-wide association studies…

GCTA
Desktop

GCTA Genome-wide Complex Trait Analysis

Estimates the variance explained by all the SNPs on a chromosome or on the…

Estimates the variance explained by all the SNPs on a chromosome or on the whole genome for a complex trait rather than testing the association of any particular SNP to the trait. We introduce…

ATHENA
Desktop

ATHENA Analysis Tool for Heritable and Environmental Network Associations

A software package that combines statistical and biological variable selection…

A software package that combines statistical and biological variable selection methods with machine learning modeling techniques to identify complex prediction models that can include non-linear…

PRSice
Desktop

PRSice Polygenic Risk Score software

Allows users to capture current standard practices in polygenic risk score…

Allows users to capture current standard practices in polygenic risk score (PRS) studies and the different applications of PRS. PRSice performs a simulation study to estimate a P-value significance…

GVCBLUP
Desktop

GVCBLUP

A powerful and versatile computing tool for assessing the type and magnitude of…

A powerful and versatile computing tool for assessing the type and magnitude of genetic effects affecting a phenotype. The GVCBLUP package is a powerful and versatile computing tool for assessing the…

SLDP
Desktop

SLDP Signed LD Profile regression

Allows quantification of genome-wide directional effect of a signed functional…

Allows quantification of genome-wide directional effect of a signed functional annotation on polygenic disease risk. SLDP detects directional effects by assessing whether the vector of marginal…

CAESAR
Desktop

CAESAR CAndidatE Search And Rank

Ranks all annotated human genes as candidates for a complex trait. CAESAR maps…

Ranks all annotated human genes as candidates for a complex trait. CAESAR maps natural language descriptions of the trait with a variety of gene-centric information sources by using ontologies, text…

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.