epigenetic-data

Genomic Interactive Visualization Engine

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

Bioinformatics16: DeepChrome: Deep-learning for predicting gene expression from histone modifications

NeurIPS17: [AttentiveChrome] Attend and Predict: Using Deep Attention Model to Understand Gene Regulation by Selective Attention on Chromatin

Snapshot: a model-free method for clustering and visualizing epigenomic data

A Python API library for exploration and data retrieval from NCBI

Tools for epigenetic data analysis

Our comprehensive database integrates data from scRNA seq and sc-ATAC seq, identifying cis-regulatory elements (CREs) through comparison with ENCODE, Epimap, GWAS Catalog, and other datasets. By connecting transcription factors (TFs), CREs, and target genes, cEpiReg unveils hidden regulatory links crucial for understanding AD pathogenesis.

R codes of the figures from the Epigenetics CSMD1 paper

Constructed a comprehensive database elucidating the intricate regulatory mechanisms underlying Alzheimer's Disease genetics, integrating scRNA-seq, scATAC-seq, CHIP-seq, CUT&RUN and eQTL data to identify cis-regulatory elements.