Bioconductor Packages

Coordinate Covariation Analysis

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Methylation array and sequencing spatial analysis methods

Quality control and analysis tools for Illumina DNA methylation BeadChip

Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models

Epigenetic Dissection of Intra-Sample-Heterogeneity

GEM: fast association study for the interplay of Gene, Environment and Methylation

Processing Various Types of Data on GEO and TCGA

Detection of scatterplots with L-shaped pattern

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

Model-based analysis of DNA methylation data

Muscle Epigenetic Age Test

Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Visual and interactive quality control of large Illumina DNA Methylation array data sets

Identify oncogenes and tumor suppressor genes from omics data

Identify oncogenes and tumor suppressor genes from omics data

Repetitive Element Methylation Prediction

RnBeads

TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Tensor Decomposition Based Unsupervised Feature Extraction

Advanced package of tensor decomposition based unsupervised feature extraction

R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors

Tools for the analysis of heterogeneous tissues

A fast scatterplot smoother suitable for microarray normalization

Controlling bias and inflation in association studies using the empirical null distribution

A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data

Illumina methylation array analysis for large experiments

Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Functional analysis of DNA methylome datasets

Methylated CpGs Set Enrichment Analysis

Discovering genomic regions where methylation is strongly associated with transcriptional activity

Missing value estimation of DNA methylation data

Estimate the cell composition of whole blood in DNA methylation samples

Analyze Illumina Infinium DNA methylation arrays

Analysing Illumina HumanMethylation BeadChip Data

Multi-Contrast Gene Set Enrichment Analysis

Preprocessing of Illumina Infinium 450K data

Placental DNA methylation analysis tools

Detection of Rare Aberrantly Methylated Regions in Array and NGS Data

Access and analyze public DNA methylation array data compilations

Summarizing Regional Methylation with Regional Principal Components Analysis

SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Interactive visualization for Illumina methylation arrays