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Differentially methylated region detection software tools | DNA methylation microarray data analysis

In addition to the single CpG analysis, a second approach can be used to perform differential methylation analysis to bring further confidence in the results. It consists in looking at regional methylation measurements rather than at single site…
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…

ChAMP
Desktop

ChAMP

Allows Illumina HumanMethylation BeadChip analysis. ChAMP is an integrated…

Allows Illumina HumanMethylation BeadChip analysis. ChAMP is an integrated analysis pipeline including functions for (i) filtering low quality probes, adjustment for Infinium I and Infinium II probe…

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…

bumphunter
Desktop

bumphunter

Allows to accomplish bump hunting in genomic data. bumphunter addresses batch…

Allows to accomplish bump hunting in genomic data. bumphunter addresses batch effects, exploits the correlation structure of the microarray data to identify differentially methylated regions (DMRs),…

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COHCAP
Desktop

COHCAP City of Hope CpG Island Analysis Pipeline

Provides tools for analysing single-nucleotide resolution methylation data.…

Provides tools for analysing single-nucleotide resolution methylation data. COHCAP is a pipeline that covers most user needs for differential methylation and integration with gene expression data.…

DM-BLD
Desktop
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QDMR
Desktop

QDMR Quantitative Differentially Methylated Region

Allows users to quantify methylation difference and identify differentially…

Allows users to quantify methylation difference and identify differentially methylated regions (DMRs) across multiple samples. QDMR is a quantitative approach genome-wide quantitative comparisons of…

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.

DMRMark
Desktop

DMRMark DMR detection based on non-homogeneous hidden Markov model

Models methylation status and detects differentially methylated regions (DMRs)…

Models methylation status and detects differentially methylated regions (DMRs) from methylation array data. DMRMark is based on non-homogeneous hidden Markov model (HMM). It can systematically pool…

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…

methylCC
Desktop

methylCC

Estimates cell composition while avoiding platforms biases. methylCC is a R…

Estimates cell composition while avoiding platforms biases. methylCC is a R package that proposes a latent variable model with region-specific and platform-dependent random effects. It permits to…

DMRcate
Desktop

DMRcate

Fits replicated methylation measurements from the Illumina HM450K BeadChip (or…

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 differentially…

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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

Identifies differentially methylated regions between unique samples using array…

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

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…

ADMIRE
Desktop
Web

ADMIRE Analysis of DNA methylation in genomic regions

Allows to analyze and visualize differential methylation in genomic regions.…

Allows to analyze and visualize differential methylation in genomic regions. ADMIRE is a semi-automatic pipeline that features five different normalization methods and performs two one-sided…

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

Implements analysis tools for DNA methylation data generated using Nimblegen…

Implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage…

Aclust
Desktop

Aclust Adjacent Site Clustering

An algorithm to detect sets of neighboring CpG sites that are correlated with…

An algorithm to detect sets of neighboring CpG sites that are correlated with each other. The R package Aclust that efficiently implements the A-clustering and the analysis pipeline is provided.

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.

NHMMfdr
Desktop

NHMMfdr

Implements False Discovery Rate (FDR) control for multiple comparisons under…

Implements False Discovery Rate (FDR) control for multiple comparisons under dependence. NHMMfdr allows to be incorporated in the model to improve detection of significant tests for informative…

ABC.RAP
Desktop

ABC.RAP Array Based CpG Region Analysis Pipeline

Identifies candidate genes that are “differentially methylated” between…

Identifies candidate genes that are “differentially methylated” between cases and controls. ABC.RAP applies Student’s t-test and delta beta analysis to identify candidate genes containing…

WangEtAl2017
Desktop

WangEtAl2017

Detects differentially methylated region (DMR). This tool uses combined signal…

Detects differentially methylated region (DMR). This tool uses combined signal from differential methylation and differential variability (DV). It can be used for case-control designs, which can…

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