phyloConverge is fast, calibrated method for identifying genomics regions underlying phenotypic convergence at high resolutionCode.
Paper: Prediction of local convergent shifts in evolutionary rates with phyloConverge characterizes the phenotypic associations and modularity of regulatory elements
NIFA is a factor analysis approach for single cell data that that generalized continuous and discrete factorsCode.
Paper: Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data
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
A suite of tools to calculate relative evolutionary rates (RERs) and their associations with phenotypes.
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.
CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations
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.
Code. Also available as part of the coloc-stats webserver.
Paper: An effective statistical evaluation of ChIPseq dataset similarity
An attention-based deep learning model to predict interacting chromosomal regions.