Dataset for "KnowYourCG: Facilitating base-level sparse methylome interpretation" --- EPICv2

Knowledgebases for the MethylationEPIC v2.0 Array (EPICv2)

This repository hosts curated knowledgebases for the Infinium MethylationEPIC v2.0 (EPICv2) array. These datasets are specifically formatted as RDS files for the knowYourCG Bioconductor package to facilitate functional enrichment analysis and technical quality control for this second-generation EPIC platform.

Technical Metadata & Quality Control

Datasets describing the physical architecture of the EPICv2 array and recommended filtering.

• ProbeType — Infinium Type I vs Type II probe design for EPICv2.

• InfiniumChemistry — Technical chemistry metadata.

• Mask — Probes flagged for technical artifacts, SNPs, or cross-reactivity specific to the v2 design.

Genomic Context & Sequence Features

Basic genomic landmarks and sequence-level characteristics.

• CGI — CpG Islands.

• nFlankCG — Flanking sequence composition.

• Tetranuc2 — Tetranucleotide frequency.

• rmsk1 — RepeatMasker repetitive elements (Set 1).

• rmsk2 — RepeatMasker repetitive elements (Set 2).

Epigenomic States & Regulatory Elements

Functional annotations for chromatin states, histone marks, and transcriptional regulation.

• ChromHMM — Chromatin state models.

• REMCChromHMM — Roadmap Epigenomics chromatin states.

• HM — Histone modification peaks.

• TFBSrm — Transcription Factor Binding Sites.

• CTCFbind — CTCF binding sites.

• ABCompartment — A/B chromatin compartments.

• PMD — Partially Methylated Domains.

Tissue Specificity & Biological Signatures

Specialized methylation phenomena and metagene summaries.

• ImprintingDMR — Imprinted gene regions (Differentially Methylated Regions).

• MetagenePC — Principal components of gene-level methylation.

External Resources

• Technical Overview: Infinium MethylationEPIC v2.0 (Illumina)

• Software: knowYourCG (Bioconductor)

• Usage Manual: Tutorial for knowYourCG Enrichment