GARDEN-NET and ChAseR: a suite of tools for the analysis of chromatin networks

Abstract

We introduce an R package and a web-based visualization tool for the representation, analysis and integration of epigenomic data in the context of 3D chromatin interaction networks. GARDEN-NET allows for the projection of user-submitted genomic features on pre-loaded chromatin interaction networks exploiting the functionalities of the ChAseR package to explore the features in combination with chromatin network topology. We demonstrate the approach on epigenomic and chromatin structure datasets in haematopoietic cells.

3D chromatin interactions involvingDrosophilainsulators are infrequent but preferential and arise before TADs and transcription

“…For each stage or condition, a specific genome scale chromatin network was built where nodes are genomic fragments and edges are significant interactions between two fragments. Then, chromatin networks were loaded on R and ChIP-seq peaks were used as features assigned to nodes using the ChAseR R package 72 (0.0.0.9) to calculate chromatin assortativity . For each feature, 1000 randomized networks preserving genomic distances and corresponding chromatin assortativity values were computed.…”