# 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:**

Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals

Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling

# 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.

Get it. 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