4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities.
basic_science · Level V
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- Record sourced from PubMed, PMID 28961756.
- Also identified by DOI 10.1093/bioinformatics/btx484.
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Abstract
The availability of powerful analysis tools will further understanding of genome organization and its relationship to phenotype in dynamical settings. The 4D Nucleome Analysis Toolbox (NAT) is a user-friendly and powerful MATLAB toolbox for time series analysis of genome-wide chromosome conformation capture (Hi-C) data and gene expression (RNA-seq). NAT can load and normalize data, define topologically associating domains, analyse translocations, produce visualization, and study time course data. We provide examples that include time series data sets and karyotypically abnormal cell lines demonstrating the flexibility of NAT. https://github.com/laseaman/4D_Nucleome_Analysis_Toolbox. indikar@umich.edu.
Medical subject headings
- Abnormal Karyotype
- Chromosomes, Human
- Gene Expression Profiling
- Genomics
- Software