Biocview "MethylationArray"

A/B compartment inference from ATAC-seq and methylation array data

Access and Analyze DNA Methylation Array Databases

Access and analyze public DNA methylation array data compilations

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

Adjust for positional and batch effects using ComBat

A fast scatterplot smoother suitable for microarray normalization

A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment

Analysing Illumina HumanMethylation BeadChip Data

Analyze Illumina Infinium DNA methylation arrays

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

BIMEGA: BIvariate Methylation and Expression GAussian mixture model

Bioc2019PanCancerStudy

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Clustering of (epigenetic) DNA methylation data using a variational Bayes NMF algorithm

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

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

Coordinate Covariation Analysis

Copy Number Analysis for 450k Illumina Methylation Arrays

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

Detection of Rare Aberrantly Methylated Regions in Array and NGS Data

Dunedin Pace of Aging Methylation Score Calculator based on Dunedin Age 45 data (DunedinPACE)

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Epigenetic Dissection of Intra-Sample-Heterogeneity

Estimate the cell composition of whole blood in DNA methylation samples

Example experimental data for use with the methyvim package

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

Get CNV information from 450K array

Identify oncogenes and tumor suppressor genes from omics data

Illumina 450K methylation array spatial analysis methods

Illumina methylation array analysis for large experiments

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Interactive visualization for Illumina methylation arrays

Lite version of EpigenCentral

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

Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions

Methylated CpGs Set Enrichment Analysis

Methylation array and sequencing spatial analysis methods

MethylMix: Identifying methylation driven cancer genes

Model-based analysis of DNA methylation data

Multi-Contrast Gene Set Enrichment Analysis

Muscle Epigenetic Age Test

Placental DNA methylation analysis tools

Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models

Preprocessing of Illumina Infinium 450K data

Processing Various Types of Data on GEO and TCGA

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quantifying the accuracy of cellular deconvolution

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Repetitive Element Methylation Prediction

RnBeads

SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Targeted, Robust, and Model-free Differential Methylation Analysis

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

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

tensorICA

Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Tools for the analysis of heterogeneous tissues

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

Biocview "MethylationArray"

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