3DGenBench: a web-server to benchmark computational models for 3D Genomics.

ABSTRACT: Modeling 3D genome organisation has been booming in the last years thanks to the availability of experimental datasets of genomic contacts. However, the field is currently missing the standardisation of methods and metrics to compare predictions and experiments. We present 3DGenBench, a web server available at https://inc-cost.eu/benchmarking/, that allows benchmarking computational models of 3D Genomics. The benchmark is performed using a manually curated dataset of 39 capture Hi-C profiles in wild type and genome-edited mouse cells, and five genome-wide Hi-C profiles in human, mouse, and Drosophila cells. 3DGenBench performs two kinds of analysis, each supplied with a specific scoring module that compares predictions of a computational method to experimental data using several metrics. W

SUBMITTER: International Nucleome Consortium 

PROVIDER: S-EPMC9252746 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature