A development environment to explore implementations of deep neural networks for predicting the relationship between transcription factor and target genes using binding and perturbation data

NetSurgeon is a novel algorithm that utilizes genome-wide gene regulatory networks to identify interventions that force a cell toward a desired expression state

Brent Lab @ WashU

Dual Threshold Optimization compares two ranked lists of features (e.g. genes) to determine the rank threshold for each list that minimizes the hypergeometric p-value of the overlap of features. It then calculates a permutation based empirical p-value and an FDR

network evaluation package

Shiny front end to yeastCallingCardsDB

A variant calling workflow suitable for both checking genotypes and processing data for BSA experiments

Gene Regulatory Network Evaluation Using Gene Ontology

Trace Recalling is a novel method for deconvoluting double traces that result from simultaneously sequencing two DNA templates. Trace Recalling identifies up to two bases at each position of such a trace.