phyloConverge

phyloConverge is fast, calibrated method for identifying genomics regions underlying phenotypic convergence at high resolution
Code.NIFA

NIFA is a factor analysis approach for single cell data that that generalized continuous and discrete factors
Code.DataRemix

DataRemix is a method for learning data transformations to optimize a non-differentiable object such as the number of eQTLs.
Code.Paper: DataRemix: a universal data transformation for optimal inference from gene expression datasets
PLIER Pathway-Level Information Extractor

PLIER is a matrix decomposition method that uses prior information from pathway databases to find an interpretable latent variable representation of gene expression datasets.
Paper: Pathway-Level Information ExtractoR (PLIER): a generative model for gene expression data
RERconverge

A suite of tools to calculate relative evolutionary rates (RERs) and their associations with phenotypes.
Application papers:
CELLCode

An R package that performs multi-layered differnetial expression analysis to account for tissue composition heterogeneity. It estimates cell-proportions, performs and correction, and assigns trascriptionally regulated genes to the tissue of origin.
DataRemix

An R package to optimize a data-normalization transform for specific biological tasks.
IntervalStats

A tool to compute associations between genomic interavals such as peaks for a ChIPseq or ATACseq dataset that uses exact enumeration to compute accurate p-values.
Code. Also available as part of the coloc-stats webserver.
Paper: An effective statistical evaluation of ChIPseq dataset similarity
EPIANN
An attention-based deep learning model to predict interacting chromosomal regions.
code