regulatory-network

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

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.

Context-sensitive creation of kinetic equations in biochemical networks

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

ChromBERT-tools: Command-line tools for ChromBERT-based regulatory analysis

Prokaryote Gene Regulatory Network (ProGRN) Inference Pipeline

doRiNa - database of posttranscriptional regulatory elements

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

Python Implementation of PROM

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

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

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

Statistical Inference for Network Centrality

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.