Shijie C Zheng1, Charles E Breeze2, Stephan Beck3, Danyue Dong1, Tianyu Zhu1, Liangxiao Ma4, Wei Ye4, Guoqing Zhang4, Andrew E Teschendorff1,3. 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/.
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/.
Authors: Alina P S Pang; Albert T Higgins-Chen; Florence Comite; Ioana Raica; Christopher Arboleda; Hannah Went; Tavis Mendez; Michael Schotsaert; Varun Dwaraka; Ryan Smith; Morgan E Levine; Lishomwa C Ndhlovu; Michael J Corley Journal: Front Genet Date: 2022-06-03 Impact factor: 4.772
Authors: Yen Ting Wong; Michael A Tayeb; Timothy C Stone; Laurence B Lovat; Andrew E Teschendorff; Rafal Iwasiow; Jeffrey M Craig Journal: Epigenetics Date: 2021-07-13 Impact factor: 4.861
Authors: Victor Yuan; Desmond Hui; Yifan Yin; Maria S Peñaherrera; Alexander G Beristain; Wendy P Robinson Journal: BMC Genomics Date: 2021-01-06 Impact factor: 3.969
Authors: Michael J Corley; Alina P S Pang; Kush Dody; Philip A Mudd; Bruce K Patterson; Harish Seethamraju; Yaron Bram; Michael J Peluso; Leonel Torres; Nikita S Iyer; Thomas A Premeaux; Stephen T Yeung; Vasuretha Chandar; Alain Borczuk; Robert E Schwartz; Timothy J Henrich; Steven G Deeks; Jonah B Sacha; Lishomwa C Ndhlovu Journal: J Leukoc Biol Date: 2021-01-19 Impact factor: 6.011
Authors: Lindsay F Rizzardi; Peter F Hickey; Adrian Idrizi; Rakel Tryggvadóttir; Colin M Callahan; Kimberly E Stephens; Sean D Taverna; Hao Zhang; Sinan Ramazanoglu; Kasper D Hansen; Andrew P Feinberg Journal: Genome Biol Date: 2021-04-22 Impact factor: 13.583
Authors: Michael J Corley; Carlo Sacdalan; Alina P S Pang; Nitiya Chomchey; Nisakorn Ratnaratorn; Victor Valcour; Eugene Kroon; Kyu S Cho; Andrew C Belden; Donn Colby; Merlin Robb; Denise Hsu; Serena Spudich; Robert Paul; Sandhya Vasan; Lishomwa C Ndhlovu Journal: PLoS Pathog Date: 2021-08-13 Impact factor: 6.823