shinyEPICo

shinyEPICo performs analysis of Illumina DNA methylation arrays (450k and EPIC) to preprocess data and identify differentially methylated positions (DMPs) and regions (DMRs) for epigenetic studies.

Key Features:

• Comprehensive analysis pipeline: Covers the workflow from raw array input through preprocessing, quality control, normalization, statistical analysis, and generation of final DMP and DMR lists.
• Preprocessing and quality control: Includes steps for probe/sample filtering and quality metrics to assess array data integrity.
• Normalization methods: Provides multiple normalization options to correct technical variation across 450k and EPIC arrays.
• Flexible statistical modeling: Supports linear-model-based testing with inclusion of covariates for adjusted differential methylation analyses.
• DMP and DMR detection: Identifies differentially methylated CpG sites (DMPs) and aggregates them into differentially methylated regions (DMRs).
• Result visualization: Generates visual summaries of quality metrics, normalization effects, and differential methylation results.
• Export for downstream analysis: Exports result tables and processed data suitable for further computational analyses.

Scientific Applications:

• Epigenetic profiling: Analysis of DNA methylation patterns in human samples using Illumina 450k and EPIC arrays.
• Differential methylation studies: Identification of CpGs and regions associated with experimental conditions or phenotypes.
• Large-cohort and multi-sample analyses: Processing and analysis of datasets with multiple samples and complex experimental designs.
• Covariate-adjusted analyses: Comparative studies requiring adjustment for confounders via linear models.
• Reproducible methylation workflows: Standardizing preprocessing, normalization, and statistical testing for reproducible results.

Methodology:

Performs preprocessing and probe/sample filtering, quality control, multiple normalization options, linear-model-based statistical testing with covariate inclusion, and identification and export of DMPs and DMRs.