methylR

methylR performs comprehensive analysis of Illumina DNA methylation array data to characterize epigenetic variation, including processing raw data, multidimensional analyses, and pathway enrichment for epigenetic studies.

Key Features:

• Integration of established packages: Leverages standard open-source packages and pipelines for methylation data analysis.
• Raw data processing and downstream analyses: Processes raw Illumina DNA methylation array data and performs downstream analyses.
• Eight-module multidimensional analysis: Provides eight distinct modules for multidimensional analysis enabling pathway enrichment and other advanced analyses.
• Array specificity: Primarily designed for Illumina DNA methylation array data.
• Accessory module adaptability: Includes accessory modules that are adaptable for analyzing different types of data.
• Validation with public datasets: Evaluated using publicly available datasets with comparisons to published outcomes.

Scientific Applications:

• Epigenetic studies: Supports analysis of DNA methylation patterns in epigenetic research.
• Gene expression regulation: Enables investigation of relationships between methylation and gene expression regulation.
• Disease mechanism studies: Facilitates study of disease mechanisms mediated by DNA methylation.
• Other epigenetic phenomena: Applicable to analysis of other biological phenomena influenced by epigenetic modifications.

Methodology:

Integrates well-established computational packages and pipelines to process raw methylation array data and generate downstream analytical outputs.