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