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Statistical and quantitative genomics

Gene set enrichment analysis: Correlation of a priori defined sets of genes with concordant differences between two biological states.
Analysis of Sample Set Enrichment Scores: Gene set enrichment analysis capturing variation across samples or individuals.
Evidence-ranked motif identification: Motif finding using side information such as gene expression or ChIP experiments.
Gene set association analysis: Correlation of a priori defined sets of genes with differential expression and genomic association between two biological states.
Bayesian sparse factor analysis of genetic covariance matrices: Estimates the additive genetic covariance matrix for high-dimensional traits. Matlab version R version, being tested
Bayesian sparse factor analysis of genetic covariance matrices: Estimates the additive genetic covariance matrix for high-dimensional traits.
Network-based Large-scale Identification oF disTal eQTL: Maps trans-expression quantitative trait loci (eQTL).
WHODAD: Paternity inference from low-coverage sequencing data.
Bayesian approximate kernel regression: Genomic selection and mapping epistatic loci.
Marginal EPIstasis Test: Mapping epistatic loci.

Morphometrics

Automated 3D Geometric Morphometrics: Aligns bones and measures distances with minimal user intervention.

Smooth Euler Characteristic Transform:An automated procedure to extract geometric or topological statistics from tumor images and software to integrate these features in a LMM.

Microbiome

Phylogenetic Isometric Log-Ratio Transform: A transform that incorporates microbial phylogenetic information and removes the artifacts associate with the analysis of compositional data.

HOst-Microbiome INteraction IDentification: Identifies associations between host genetic variation and microbiome taxonomic composition.

Machine learning and statistics

Localized sliced inverse regression: Nonlinear supervised dimension reduction based on generalized eigendecomposition. Also Russian translation of this page courtesy of Starmoz
Bayesian mixture of inverses: Probabilistic model based method for supervised dimension reduction.
Bayesian gradient learning: Supervised dimension reduction via inference of the gradient of the regression or classification function.
Kernel sliced inverse regression: Kernel version of sliced inverse regression.
Bayesian group factor Analysis with Structured Sparsity (BASS): Bayesian model that extends cannonical correlation analysis to multiple groups.
Moment Estimation for Latent Dirichlet models (MELD): Generalized method of moments estimator for admixture models with mixed data types..