Genetic correlation estimation and multi-trait analysis
GNOVA
Powerful and annotation-stratified genetic covariance estimation using GWAS summary statistics
SUPERGNOVA
A statistically principled and robust method for local genetic correlation analysis using GWAS summary statistics
LOGODetect
A scan statistic approach to identify precise genome regions with local genetic correlation for multiple traits
PARSEC
A variance component framework to partition heritability and genetic covariance by direct and indirect effect paths
EncoreDNM
Quantifying correlated enrichment of de novo mutations in multiple disorders
GSUB
A close-form approach to performing GWAS-by-subtraction
Gene-environment interaction and social genomics
PIGEON
A variance component analytical framework for quantifying and estimating polygenic gene-environment interaction for human complex traits
QUAIL
A quantile regression framework to estimate genetic effects on phenotypic variability
PENGUIN
Controlling for polygenic genetic confounding in epidemiologic association analysis
DONUTS
A method to estimate direct and indirect genetic effects from multi-generational GWAS summary statistics
Genetic risk prediction
X-Wing
Estimating cross-ancestry local genetic correlation and improving risk prediction accuracy with GWAS summary statistics
PUMAS
A tool for polygenic risk score model fine-tuning using GWAS summary statistics alone
AnnoPred
An empirical Bayesian framework that uses integrative functional annotations to improve risk prediction accuracy
Machine learning-assisted statistical inference
Genome Annotation
GenoCanyon
An unsupervised learning framework to predict functional DNA elements in the human genome.
GenoSkyline
Predict tissue-specific functional regions in the human genome through integration of data from Roadmap Epigenomics Project.
GenoSkyline-Plus
A substantial upgrade of GenoSkyline, available for all 127 tissue and cell types from Roadmap Epigenomics Project.
Other methods for GWAS and sequencing analysis
UTMOST
Cross-tissue gene expression imputation and transcriptome-wide association analysis using GWAS summary statistics
TITANS
A computational tool for conducting transcriptome-wide association study in proband-parent trios
BADGERS
Polygenic score-based biobank-wide association scans using GWAS summary statistics
ORIGAMI
A computational framework to simulate offspring genotype data from parental genomes
GenoWAP
Functional SNP reprioritization through integrative analysis of GWAS summary statistics and functional annotations