EagleC Explorer: A desktop application for interactively detecting and visualizing SVs and enhancer hijacking on Hi-C contact maps.
Yihao FuXiao-Tao WangFeng YuePublished in: bioRxiv : the preprint server for biology (2023)
It has been shown that Hi-C can be used as a powerful tool to detect structural variations (SVs) and enhancer hijacking events. However, there has been no existing programs that can directly visualize and detect such events on a personal computer, which hinders the broad adaption of the technology for intuitive discovery in cancer studies. Here, we introduce the EagleC Explorer, a desktop software that is specifically designed for exploring Hi-C and other chromatin contact data in cancer genomes. EagleC Explorer has a set of unique features, including 1) conveniently visualizing global and local Hi-C data; 2) interactively detecting SVs on a Hi-C map for any user-selected region on screen within seconds, using a deep-learning model; 3) reconstructing local Hi-C map surrounding user-provided SVs and generating publication-quality figures; 4) detecting enhancer hijacking events for any user-suggested regions on screen. In addition, EagleC Explorer can also incorporate other genomic tracks such as RNA-Seq or ChIP-Seq to facilitate scientists for integrative data analysis and making novel discoveries.
Keyphrases
- data analysis
- rna seq
- high throughput
- single cell
- deep learning
- transcription factor
- papillary thyroid
- binding protein
- squamous cell
- electronic health record
- genome wide
- small molecule
- gene expression
- public health
- big data
- dna damage
- squamous cell carcinoma
- living cells
- young adults
- childhood cancer
- convolutional neural network
- oxidative stress