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Chikina Lab

phyloConverge

phyloConverge

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

Code.

Paper: Prediction of local convergent shifts in evolutionary rates with phyloConverge characterizes the phenotypic associations and modularity of regulatory elements

NIFA

DataRemix

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

Code.

Paper: Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data

DataRemix

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

PLIER is a matrix decomposition method that uses prior information from pathway databases to find an interpretable latent variable representation of gene expression datasets.

Try it and get it.

Paper: Pathway-Level Information ExtractoR (PLIER): a generative model for gene expression data

RERconverge

RERconverge

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

Code.



Application papers:

  • Pan-mammalian analysis of molecular constraints underlying extended lifespan
  • 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

    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.

    Code.

    Paper:
    CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations

    DataRemix

    DataRemix

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

    Code.

    IntervalStats

    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