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
CelloType: Simultaneous cell/nuclear segmentation and cell type annotation of spatial omics data