Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Differential methylation site detection software tools | DNA methylation microarray data analysis

After correct preprocessing of the data (i.e. filtering out problematic probes and normalizing the data), differential methylation analysis can be performed. Generally, the first approach consists in a single-probe analysis. Statistical tests (such…
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…

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…

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…

MethLAB
Desktop

MethLAB

Performs analyses of array-based DNA methylation data. MethLAB is a graphical…

Performs analyses of array-based DNA methylation data. MethLAB is a graphical user interface (GUI) package. For each cytosine–phosphate–guanine (CpG) site, the software models methylation as a…

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.

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…

methylDMV
Desktop

methylDMV

Allows to incorporate adjustment for confounding variables that potentially…

Allows to incorporate adjustment for confounding variables that potentially affect methylation levels. methylDMV works about simultaneous detection of differential mean (DM) and differential…

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…

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…

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…

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…

G T A T C G C T A
Fitnoise
Desktop

Fitnoise

Allows users to perform Empirical Bayesian linear modelling. Fitnoise…

Allows users to perform Empirical Bayesian linear modelling. Fitnoise authorizes to experiment measurements related with genes or genomic features by deducing differential expression testing. The…

Qlucore Omics…
Desktop

Qlucore Omics Explorer

Provides bioinformatics products to support the user with visual analysis of…

Provides bioinformatics products to support the user with visual analysis of measured data taking into account publicly available information such as gene ontologies, pathways and other system…

Information

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