epihet

The 'epihet' software tool is an R package developed to automate the intra-tumoral epigenetic allelic heterogeneity measurement. Intra-tumoral epigenetic heterogeneity is an essential indicator of tumor population fitness, associated with transcriptional deregulation. 'epihet' facilitates the calculation of intra-tumoral epigenetic heterogeneity and enables differential epigenetic heterogeneity analysis. Additionally, the tool can perform biological network analysis to transform cancer-specific differential epigenetic heterogeneity loci into cancer-related biological functions and clinical biomarkers. The utility of 'epihet' is demonstrated using acute myeloid leukemia data.

Topic

Epigenetics;Methylated DNA immunoprecipitation;Workflows

Detail

  • Operation: Principal component visualisation;Principal component analysis;Network analysis;Enrichment analysis;Differential gene expression profiling;Heat map generation

  • Software interface: Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.4.0

  • Credit: The Jackson Laboratory for Genomic Medicine, Leukemia Research Foundation New Investigator Grant, The Jackson Laboratory Director’s Innovation fund, The Jackson Laboratory Cancer Center New Investigator Award, The Jackson Laboratory Cancer Center Fast Forward Award, the National Institute of General Medical Sciences of the National Institutes of Health, the Jackson Laboratory for Mammalian Genetics, the National Cancer Institute of the National Institutes of Health.

  • Input: -

  • Output: -

  • Contact: Sheng Li sheng.li@jax.org ,Xiaowen Chen Xiaowen.Chen@jax.org

  • Collection: -

  • Maturity: Stable

Publications

  • epihet for intra-tumoral epigenetic heterogeneity analysis and visualization.
  • Chen X, et al. epihet for intra-tumoral epigenetic heterogeneity analysis and visualization. epihet for intra-tumoral epigenetic heterogeneity analysis and visualization. 2021; 11:376. doi: 10.1038/s41598-020-79627-x
  • https://doi.org/10.1038/S41598-020-79627-X
  • PMID: 33432081
  • PMC: PMC7801679

Download and documentation

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