shinyEPICo

"shinyÉPICo" is an interactive, web-based, and graphical tool designed to analyze Illumina DNA methylation arrays, specifically 450k and EPIC arrays. The tool provides a user-friendly interface, allowing users to analyze data from their computers or servers. shinyÉPICo covers the entire analysis workflow, from raw data to the final list of differentially methylated positions and regions, and facilitates testing various normalization methods, linear model parameters, and CpG filters. It offers interactive graphics to aid in selecting options at each step, making DNA methylation analysis more standardized, efficient, and accessible for laboratories studying DNA methylation.

Topic

Microarray experiment;Epigenetics;DNA;Methylated DNA immunoprecipitation;Workflows

Detail

  • Operation: Methylation analysis;Standardisation and normalisation;Scatter plot plotting

  • Software interface: Command-line tool,Library,Web API

  • Language: R

  • License: GNU Affero General Public License v 3.0

  • Cost: Free

  • Version name: 1.10.0

  • Credit: The Spanish Ministry of Science and Innovation, i-PFIS PhD fellowship from Acción Estratégica en Salud, Fondo Social Europeo.

  • Input: -

  • Output: -

  • Contact: Octavio Morante-Palacios octaviompa@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • shinyÉPICo: a graphical pipeline to analyze Illumina DNA methylation arrays.
  • Morante-Palacios O and Ballestar E. shinyÉPICo: a graphical pipeline to analyze Illumina DNA methylation arrays. shinyÉPICo: a graphical pipeline to analyze Illumina DNA methylation arrays. 2021; 37:257-259. doi: 10.1093/bioinformatics/btaa1095
  • https://doi.org/10.1093/BIOINFORMATICS/BTAA1095
  • PMID: 33416853
  • PMC: -

Download and documentation

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