All-in-one analysis pipeline

A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.

Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data

Network Regression Embeddings reveal cell-type Transcription Factor coordination for target gene (TG) regulation

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

Multi-omics Systems-Level Interactive Data Exploration (multiSLIDE)

Multitask Learning for Transcriptional Regulatory Network Inference in Julia

Reconstruct a Transcriptional Regulatory Network using the principle of Maximum Entropy.

Database of HTH-DNA complexes

This repository is the code source for the RegOmics tool - Regulatory extraction for Omics data.

A package to identify functional TFBS

Integrating the transcriptional regulatory network with genome-scale metabolic models.

Screen tf motif within provided regions.

Gibbs 3.2 formerly located at http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html