DNA methylation array analysis steps

DNA methylation is involved in numerous physiological processes and also disease states, such as cancer (Jones, 2012). This has raised wide interest in developing large-scale DNA methylation profiling microarray technologies to improve our molecular understanding of diseases.…

DNA methylation microarray data analysis bioinformatics software tools

FastDMA
Desktop

FastDMA

A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which…

A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing.

RnBeads
Desktop

RnBeads

An R package for comprehensive analysis of DNA methylation data obtained with…

An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite…

SWAN
Desktop

SWAN Subset-quantile Within Array Normalization

A within array normalization method that substantially reduces the technical…

A within array normalization method that substantially reduces the technical variability between the probe types whilst maintaining the important biological differences. The SWAN method makes the…

lumi
Desktop

lumi

Provides class infrastructure and associated methods to construct an Illumina…

Provides class infrastructure and associated methods to construct an Illumina analysis workflow pipeline starting with raw data through functional analysis. Besides supporting the existing algorithms…

minfi
Desktop

minfi

A suite of computational tools that incorporate state-of-the-art statistical…

A suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. minfi provides methods for preprocessing, quality assessment and detection of…

limma
Desktop

limma Linear Models for Microarray Data

Provides an integrated solution for analysing data from gene expression…

Provides an integrated solution for analysing data from gene expression experiments. limma contains rich features for handling complex experimental designs and for information borrowing to overcome…

ChAMP
Desktop

ChAMP

Methylumi
Desktop

Methylumi

A package that provides classes for holding and manipulating Illumina…

A package that provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices…

missMethyl
Desktop

missMethyl

Performs normalisation, removal of unwanted variation in differential…

Performs normalisation, removal of unwanted variation in differential methylation analysis, differential variability testing and gene set analysis for the 450K array. The functions have been written…

wateRmelon
Desktop

wateRmelon

A user-friendly software package compatible with the existing methylumi, minfi…

A user-friendly software package compatible with the existing methylumi, minfi and IMA packages, that allows others to utilize the same normalization methods and data quality tests on 450K data.

CpGassoc
Desktop

CpGassoc

An R package that can efficiently perform the statistical analysis needed for…

An R package that can efficiently perform the statistical analysis needed for increasingly large methylation datasets. CpGassoc can perform standard analyses of large datasets very quickly with no…

DM-BLD
Desktop
ENmix
Desktop

ENmix

A package that provides a background correction method which uses a mixture of…

A package that provides a background correction method which uses a mixture of exponential and truncated normal distributions to flexibly model signal intensity and uses a truncated normal…

G T A T C G C T A
quantro
Desktop

quantro

Provides a data-driven solution to test the assumptions of global normalization…

Provides a data-driven solution to test the assumptions of global normalization methods. Group level information about each sample (such as tumor/normal status) must be provided because the test…

InCroMAP
Desktop

InCroMAP Integrated analysis of Cross-platform MicroArray and Pathway data

A tool for the analysis and visualization of high-level microarray data from…

A tool for the analysis and visualization of high-level microarray data from individual or multiple different platforms. Currently, InCroMAP supports mRNA, microRNA, DNA methylation and protein…

IMGui
Desktop

IMGui

Provides a graphical user interface (GUI) for the latest Isolation with…

Provides a graphical user interface (GUI) for the latest Isolation with Migration (IM) program. IMGui provides a comprehensive set of tools for performing demographic analyses, tracking progress of…

BMIQ
Desktop

BMIQ

Beta Mixture Quantile Method for normalisation of Illumina Infinium 450k data.

Beta Mixture Quantile Method for normalisation of Illumina Infinium 450k data.

RUVm
Desktop

RUVm

A versatile method that effectively accounts for unwanted variation in DM…

A versatile method that effectively accounts for unwanted variation in DM analyses of 450k data across a wide variety of studies. RUVm performs particularly well in situations where the sources of…

oxBS-MLE
Desktop

oxBS-MLE oxidative bisulfite Maximum Likelihood Estimate

An efficient method based on binomial modeling of paired bisulfite and…

An efficient method based on binomial modeling of paired bisulfite and oxidative bisulfite data from sequencing or array analysis. Evaluation in several datasets showed that oxBS-MLE outperformed…

OxyBS
Desktop

OxyBS

A method using maximum likelihood estimation to accurately estimate the…

A method using maximum likelihood estimation to accurately estimate the parameters of unmethylated cytosine (5C), 5mC and 5hmC from Infinium microarray data given the signal intensities from the oxBS…

LR450K
Desktop

LR450K

A computational strategy to predict DNA methylation by integrating cell-type…

A computational strategy to predict DNA methylation by integrating cell-type specific 450K array data and common DNA sequence features. We developed a computational model that is trained on 14…

CopyNumber450kC…
Desktop

CopyNumber450kCancer

Provides a novel functionality to correct the center in segmentation data…

Provides a novel functionality to correct the center in segmentation data obtained from copy number calling tools such as CopyNumber450k and ChAMP. CopyNumber450kCancer implements the maximum density…

IMA
Desktop

IMA

A package designed to automate the pipeline for analyzing site-level and…

A package designed to automate the pipeline for analyzing site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray.

DiffVar
Desktop

DiffVar

Detects differential variability for individual CpG sites in methylation data.…

Detects differential variability for individual CpG sites in methylation data. DiffVar employs an empirical Bayes model framework that can take into account any experimental design and is robust to…

quantroSim
Desktop

quantroSim

An R-package to simulate gene expression and DNA methylation data. The…

An R-package to simulate gene expression and DNA methylation data. The R-package quantroSim is the supporting data simulation package for the quantro R/Bioconductor package which can be used to…

WFMM
Desktop

WFMM Wavelet-Based Functional Mixed Models

A Windows command-line application that implements a Bayesian wavelet-based…

A Windows command-line application that implements a Bayesian wavelet-based functional mixed model methodology for functional data analysis. WFMM can be generally applied to any complex functional…

MethLAB
Desktop

MethLAB

A GUI package for analysis of DNA methylation microarray data.

A GUI package for analysis of DNA methylation microarray data.

Probe Lasso
Desktop

Probe Lasso

A method for calling DMRs using Illumina 450K Methylation BeadChip arrays…

A method for calling DMRs using Illumina 450K Methylation BeadChip arrays implemented as part of suite of functions in the Bioconductor package ChAMP – an all-in-one analysis pipeline that takes…

DiMmeR
Desktop

DiMmeR Discovery of Multiple Differentially Methylated Regions

Guides scientists the whole way through EWAS data analysis. DiMmer offers…

Guides scientists the whole way through EWAS data analysis. DiMmer offers parallelized statistical methods for identifying DMRs in both Illumina 450K and 850K EPIC chip data and also methylated…

seqlm
Desktop

seqlm

A method for identifying differentially methylated regions. First, the data is…

A method for identifying differentially methylated regions. First, the data is divided into smaller segments based on genomic distance between consecutive probes. Then, each of these segments is…

D3M
Desktop

D3M

A method for detection of differential distribution of methylation, based on…

A method for detection of differential distribution of methylation, based on distribution-valued data. D3M can detect the differences in high-order moments, such as shapes of underlying distributions…

G T A T C G C T A
PINCAGE
Desktop

PINCAGE Probabilistic INTegration of CAncer GEnomics data

Uses probabilistic integration of cancer genomics data for combined evaluation…

Uses probabilistic integration of cancer genomics data for combined evaluation of RNA-seq gene expression and 450K array DNA methylation measurements of promoters as well as gene bodies. The method…

funtooNorm
Desktop

funtooNorm

An R package for normalization of data from the Illumina Infinium Human…

An R package for normalization of data from the Illumina Infinium Human Methylation450 BeadChip (Illumina 450 K) built on the concepts in the recently published funNorm method, and introducing…

MethylAid
Desktop

MethylAid

Provides complete insight in the quality of each sample in a large-scale EWAS…

Provides complete insight in the quality of each sample in a large-scale EWAS and gives the user full control on the selection of bad-quality samples that should be excluded from downstream analyses.…

Marmal-aid
Desktop
Web

Marmal-aid

A combined database and R package that allows you to investigate the…

A combined database and R package that allows you to investigate the methylation state of regions of interest across the genome. Marmal-aid is the largest publicly available Illumina…

cnAnalysis450k
Desktop

cnAnalysis450k

Realizes the normalization, segmentation and aggregation of Illumina…

Realizes the normalization, segmentation and aggregation of Illumina methylation array copy number (CN) data (450k + EPIC). CnAnalysis450k allows to directly compare any preprocessed CN data. It…

DMRcate
Desktop

DMRcate

A package that fits replicated methylation measurements from the Illumina…

A package that fits replicated methylation measurements from the Illumina HM450K BeadChip (or 450K array) spatially across the genome using a Gaussian kernel. DMRcate identifies and ranks the most…

G T A T C G C T A
comb-p
Desktop

comb-p combined-pvalues

A command-line tool and a python library that manipulates BED files of possibly…

A command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false…

DMRforPairs
Desktop

DMRforPairs

Identifying differentially methylated regions between unique samples using…

Identifying differentially methylated regions between unique samples using array based methylation profiles.

NIMBL
Desktop

NIMBL Numerical Identification of Methylation Biomarker Lists

MATLAB code to quality control and prioritize differentially methylated markers…

MATLAB code to quality control and prioritize differentially methylated markers from illumina infinium arrays.

PyMAP
Desktop

PyMAP

A native python module for analysis of 450k methylation platform. PyMAP can be…

A native python module for analysis of 450k methylation platform. PyMAP can be easily deployed to cloud platforms that support python scripting language for large-scale methylation studies. By…

ICDMR
Desktop

ICDMR Identification of Consistently Differentially Methylated Regions

Analyzes methylation intensity data generated from tiling arrays to locate DMRs…

Analyzes methylation intensity data generated from tiling arrays to locate DMRs across a large set of samples simultaneously. ICDMR provides a way to calculate the concordance between adjacent…

conumee
Desktop

conumee

Enhanced copy-number variation analysis using Illumina 450k methylation arrays.…

Enhanced copy-number variation analysis using Illumina 450k methylation arrays. conumee contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using…

MultiDataSet
Desktop

MultiDataSet

MultiDataSet is designed for integrating multi omics data sets and…

MultiDataSet is designed for integrating multi omics data sets and MethylationSet to contain normalized methylation data. These package contains base classes for MEAL and rexposome packages. By…

illuminaio
Desktop

illuminaio

A package that parses IDAT files from any BeadArray platform, including the…

A package that parses IDAT files from any BeadArray platform, including the decryption of files from Illumina’s gene expression arrays. illuminaio provides the first open-source package for this…

ARRmNormalizati…
Desktop

ARRmNormalization

A package that performs the Adaptive Robust Regression method (ARRm) for the…

A package that performs the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

methyAnalysis
Desktop

methyAnalysis

A package that aims for the DNA methylation data analysis and visualization. A…

A package that aims for the DNA methylation data analysis and visualization. A MethyGenoSet class is defined to keep the chromosome location information together with the data. methyAnalysis also…

charm
Desktop

charm

This package implements analysis tools for DNA methylation data generated using…

This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol.

shinyMethyl
Desktop

shinyMethyl

A Bioconductor package for interactive quality control of DNA methylation data…

A Bioconductor package for interactive quality control of DNA methylation data from Illumina 450k arrays. The package summarizes 450k experiments into small exportable R objects from which an…

BioTile
Desktop

BioTile

A Perl based tool for the identification of differentially enriched regions in…

A Perl based tool for the identification of differentially enriched regions in tiling microarray data.

ADMIRE
Desktop
Web

ADMIRE Analysis of DNA methylation in genomic regions

An open source, semi-automatic analysis pipeline and visualization tool for…

An open source, semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450 Assays with a focus on ease of use. ADMIRE features arbitrary experimental settings, quality…

Qlucore Omics…
Desktop

Qlucore Omics Explorer

A next-generation bioinformatics software that combines powerful statistical…

A next-generation bioinformatics software that combines powerful statistical methods with real time visualization and an intuitive user interface.

GenomeStudio
Desktop

GenomeStudio

Visualize and analyze data generated on Illumina array platforms. GenomeStudio…

Visualize and analyze data generated on Illumina array platforms. GenomeStudio supports the primary analysis of microarray data. Performance-optimized tools and a user-friendly graphical interface…

les
Desktop

les

Estimates Loci of Enhanced Significance (LES) in tiling microarray data.

Estimates Loci of Enhanced Significance (LES) in tiling microarray data.

Related Websites
Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.