Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data

A unified framework for discovering, analyzing, integrating, and visualizing regulatory motifs and transcription factor binding sites across bulk, single-cell, and long-read sequencing modalities.

Integrative analysis workshop with TCGAbiolinks and ELMER

Context-sensitive creation of kinetic equations in biochemical networks

An R package designed to integrate and visualize various levels of epigenomic information, including but not limited to: ChIP, Histone, ATAC, and RNA sequencing. epiRomics is also designed to identify enhancer and enhanceosome regions from these data.

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

MSLCRN: a novel step-wise method for inferring module-specific lncRNA-mRNA causal regulatory network in human cancer

doRiNa - database of posttranscriptional regulatory elements

CMTCN: A web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks

Prokaryote Gene Regulatory Network (ProGRN) Inference Pipeline

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

Statistical Inference for Network Centrality

Hub and Spoke Landing Zone for either Azure Commercial or Azure Government scenarios.

Python Implementation of PROM

DECODER-SC is an R-based algorithm for quantifying regulatory execution failure by measuring discordance between transcription factor activity and target gene expression in single-cell RNA-seq data.

ASP-based attractor computation

Supplemental scripts and analyses for the SINGE manuscript

A package that ranks the SNPs using genomic, epigenomic and network based features.

A minimal Python library for gene regulatory network inference.

A novel insight into neurological disorders through HDAC6 protein-protein interactions