Software can be also be downloaded from GitHub Here.

CSI-ANN: Discover functional DNA elements based on their epigenetic profiles

miPALM: Infer gene modules from molecular interaction networks

CoSBI: Identify combinatorial chromatin modification patterns across genomic loci

MAPIT: Identify deregulated molecular pathways by integrating expression, DNA methylation, and protein-protein interaction data

SS-CoSBI: Identify combinatorial chromatin modification patterns by semi-supervised biclustering

FCOP: Identify context-specific combinatorial interactions among transcription factors using ChIP-Seq data

IM-PET: Identify target promoters of distal transcriptional enhancers by integrating multiple types of genomics data

M-Module: Simultaneous analysis of multiple functional gene networks to identify shared and network-specific modules

4DGenome: a comprehensive database of chromatin interactions

EnhancerAtlas: a resource for enhancer annotation and analysis in human cells and tissues

CD8T-TRNs: Epigenomics-based reconstruction of transcriptional regulatory network of CD8+ T cells in response to infection

GMAP: Identify hierarchical chromatin domains using Hi-C data

OptiCon: Predict synergistic key regulators in a gene regulatory network

LiMACC: Identify statistically significant chromatin interactions using Capture-C/Capture-Hi-C data

ARVIN: Identifying noncoding risk variants using disease-relevant gene regulatory networks

SCRABBLE: Single-cell RNA-Seq imputation constrained by bulk RNA-Seq data

VisCello Software platform for hosting and interactive analysis and visualizaiton of single cell data

scATAC-pro:  Comprehensive workbench for single-cell chromatin accessibility sequencing data

PANGEA: Identify risk noncoding mutations by joint analysis of mutation and gene expression data

MAPLE: Predictive modeling of single-cell DNA methylation data

CytoTalk: De novo construction of signaling pathways using single-cell transcriptomics data

GLUER: Integration of single-cell omics and image data

CytoCommunity: Supervised and unsupervised discovery of tissue cellular neighborhoods