EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI

Shijie C Zheng; Charles E Breeze; Stephan Beck; Danyue Dong; Tianyu Zhu; Liangxiao Ma; Wei Ye; Guoqing Zhang; Andrew E Teschendorff

doi:10.1093/bioinformatics/btz833

EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI

Bioinformatics. 2019 Nov 9;36(6):1950-1951. doi: 10.1093/bioinformatics/btz833. Online ahead of print.

Authors

Shijie C Zheng¹, Charles E Breeze², Stephan Beck³, Danyue Dong¹, Tianyu Zhu¹, Liangxiao Ma⁴, Wei Ye⁴, Guoqing Zhang⁴, Andrew E Teschendorff^{1

3}

Affiliations

¹ CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China.
² Altius Institute for Biomedical Sciences, Seattle, WA, USA.
³ UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom.
⁴ Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China.

Abstract

Summary: It is well recognized that cell-type heterogeneity hampers the interpretation of Epigenome-Wide Association Studies (EWAS). Many tools have emerged to address this issue, including several R/Bioconductor packages that infer cell-type composition. Here we present a web application for cell-type deconvolution, which offers the functionality of our EpiDISH Bioconductor/R package in a user-friendly GUI environment. Users can upload their data to infer cell-type composition and differentially methylated cytosines in individual cell-types (DMCTs) for a range of different tissues.

Availability and implementation: EpiDISH web server is implemented with Shiny in R, and is freely available at https://www.biosino.org/EpiDISH/.