Evaluates Hi-C data to identify enriched DNA-DNA interactions. PSYCHIC analyzes promoter-enhancer interactions through three steps: (1) it finds an optimal segmentation of each chromosome into topological domains via a unified probalistic model and a dynamic programming algorithm; (2) it iteratively combines neighboring domains into hierarchical structures and finally (3) it matches each domain by using a topologically association domain (TAD) -specific background model.
A high-throughput identification pipeline for promoter interacting enhancer element to streamline the workflow from mapping raw Hi-C reads, identifying DNA-DNA interacting fragments with high confidence and quality control, detecting histone modifications and DNase hypersensitive enrichments in putative enhancer elements, to ultimately extracting possible intra- and inter-chromosomal enhancer-target gene relationships.
Enables epigenomic imputation. Avocado is a model that compresses epigenomic data into a complex representation of the human genome. It employs multi-scale deep tensor factorization with the aim of furnishing an increased imputation of epigenomic tracks. The model was developed to supply users with latent representations that encodes most peaks, and which can assist users in performing prediction tasks.
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