methylation-microarrays

A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays

Python toolkit for parsing, processing, and analysis of Illumina methylation array IDAT files

Regional Association of DNA Methylome variability with the Exposome and geNome (RAMEN) is an R package which goal is to identify Variable Methylated Loci (VML) in microarray DNA methylation data. Then, using genome (G) and exposome (E) data, it can identify which individual (G or E) or joint (G+E or GxE) model better explains the VML variability.

This package provides Illumina Mouse Methylation Array Manifest (12.v1, Genome Build mm10) compatible with minfi.

Gaussian mixture modelling - Unsupervised learning

Methylation Array Cross-Reactive Probes

📦 🔬 R/methyvim: Targeted, Robust, and Model-free Differential Methylation Analysis

DNA methylation (DNAm) Bioconductor package for Illumina Methylation arrays (EPICv2, EPIC and 450K). DOI: 10.18129/B9.bioc.dnaEPICO

Epicopy R package for CNV identification from methylation microarrays.

Integrative analysis of differential DNA methylation and TFAP2α binding sites in non-small cell lung cancer using Illumina 450K microarrays and ChIP-seq data.

📦 Bioconductor data package associated with the methyvim R package

An algorithm made in R markdown that assures that the microarray is randomized without any bias.

generates reference matrix of average beta methylation values

An annotation for mapping cpgs on the EPIC DNA methylation microarray platform to genomic features.

EpicopyData companion data package for Epicopy.

MethylSeg is a context-aware methylome segmentation framework for identifying Highly, Intermediately, Partially, and Lowly methylated domains.

MONTE:Methylation-based Observation Normalizationand Tumor purity Estimation

Detection of rare aberrantly methylated regions / epimutations in array and NGS data — an R/Bioc package

MONTE:Methylation-based Observation Normalizationand Tumor purity Estimation