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

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

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

Dual threshold optimization for identifying convergent evidence: TF binding locations and TF perturbation responses.

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

Multitask Learning for Transcriptional Regulatory Network Inference in Julia

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

Screen tf motif within provided regions.

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

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

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