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.
A suite of tools to calculate relative evolutionary rates (RERs) and their associations with phenotypes.
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
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.
An R package to optimize a data-normalization transform for specific biological tasks.
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.
An attention-based deep learning model to predict interacting chromosomal regions.