DNA methylation microarray data analysis bioinformatics software tools

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
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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
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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…

minfi
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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…

Methylumi
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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…

IMA
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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.

InCroMAP
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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…

lumi
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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…

limma
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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…

CpGassoc
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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…

MethLAB
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MethLAB

A GUI package for analysis of DNA methylation microarray data.

A GUI package for analysis of DNA methylation microarray data.

Marmal-aid
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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…

DM-BLD
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conumee
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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
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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…

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comb-p
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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…

OxyBS
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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
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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…
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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…

MethylAid
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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.…

SWAN
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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…

BioTile
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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.

DiMmeR
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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…

PyMAP
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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
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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…

oxBS-MLE
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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…

seqlm
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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
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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…

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PINCAGE
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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
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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…

WFMM
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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…

DiffVar
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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…

ENmix
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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…

ADMIRE
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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…

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quantro
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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…

quantroSim
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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…

RUVm
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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…

illuminaio
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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…

shinyMethyl
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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…

Probe Lasso
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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…

missMethyl
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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…

DMRcate
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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…

Qlucore Omics…
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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.

DMRforPairs
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DMRforPairs

Identifying differentially methylated regions between unique samples using…

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

BMIQ
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BMIQ

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

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

NIMBL
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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.

ARRmNormalizati…
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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
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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…

wateRmelon
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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.

ChAMP
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ChAMP

A package that includes quality control metrics, a selection of normalization…

A package that includes quality control metrics, a selection of normalization methods and methods to identify differentially methylated regions and to highlight copy number alterations. In addition…

GenomeStudio
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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…

charm
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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.

les
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les

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

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

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