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

DNA methylation tools

Epigenetic mechanisms, including DNA methylation, are responsible for determining and maintaining cell fate, stably differentiating the various tissues in our bodies. Increasing evidence shows that DNA methylation plays a significant role in cancer,…
BS Seeker
Desktop
Web

BS Seeker

Allows to map the bisulfite-treated short reads. BS Seeker is a bisulfite…

Allows to map the bisulfite-treated short reads. BS Seeker is a bisulfite sequencing (BS) alignment tool that performs genome indexing, read alignment and DNA methylation levels calling for each…

CGmapTools
Desktop

CGmapTools

Provides a standard for bisulfite sequencing data related manipulation.…

Provides a standard for bisulfite sequencing data related manipulation. CGmapTools is a command-line bisulfite sequencing analysis toolkit with enhanced features on single-nucleotide variant (SNV)…

The Apple…
Dataset

The Apple Genome and Epigenome

Gives access to the apple genome. The Apple Genome and Epigenome contains up to…

Gives access to the apple genome. The Apple Genome and Epigenome contains up to date gene annotation, transposable element (TE) annotation, genetic markers, DNA methylation data, small RNA data and…

NGSmethDB
Dataset

NGSmethDB

A repository for single-base whole-genome methylome maps for the best-assembled…

A repository for single-base whole-genome methylome maps for the best-assembled eukaryotic genomes. NGSmethDB is a database with a very broad scope to facilitate the analysis of methylation data from…

Epigram
Desktop

Epigram

Predicts histone modification and DNA methylation patterns from DNA motifs.…

Predicts histone modification and DNA methylation patterns from DNA motifs. Epigram is an analysis pipeline used to systematically identify DNA motifs that are predictive of epigenomic modifications.…

DiseaseMeth
Dataset

DiseaseMeth

Presents the most complete collection and annotation of aberrant DNA…

Presents the most complete collection and annotation of aberrant DNA methylation in human diseases, especially various cancers. DiseaseMeth is focused not only on curated information about diseases,…

MethSMRT
Dataset

MethSMRT Methylomes Single-Molecule Real-Time

A database about DNA 6mA and 4mC methylomes. MethSMRT provides tools to store,…

A database about DNA 6mA and 4mC methylomes. MethSMRT provides tools to store, browse, search and download epigenome-wide methylation profiles of 156 species, including seven eukaryotes such as…

MethylMix
Desktop

MethylMix

An algorithm implemented in R to identify disease specific hyper and…

An algorithm implemented in R to identify disease specific hyper and hypomethylated genes. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal…

ELMER
Desktop

ELMER Enhancer Linking by Methylation/Expression Relationships

An R-based tool that uses DNA methylation to identify enhancers and correlates…

An R-based tool that uses DNA methylation to identify enhancers and correlates enhancer state with expression of nearby genes to identify transcriptional targets. Transcription factor motif analysis…

PubMeth
Dataset

PubMeth

A cancer methylation database that includes genes that are reported to be…

A cancer methylation database that includes genes that are reported to be methylated in various cancer types. A query can be based either on genes (to check in which cancer types the genes are…

G T A T C G C T A
EpiExplorer
Web

EpiExplorer

A web tool that allows you to use large reference epigenome datasets for your…

A web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborious preprocessing.

MethyCancer
Dataset

MethyCancer

It is developed to study interplay of DNA methylation, gene expression and…

It is developed to study interplay of DNA methylation, gene expression and cancer. It hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from…

MethPed
Desktop

MethPed

Allows researchers and clinical diagnosticians to test single samples as well…

Allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. In the current version of MethPed the following…

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…

GED
Dataset

GED Gametogenesis Epigenetic modification Database

A comprehensive resource of epigenetic modification of gametogenesis. Users can…

A comprehensive resource of epigenetic modification of gametogenesis. Users can get the information about epigenetic modifications (DNA methylation, histone modification and miRNA regulation) and the…

MethylomeDB
Dataset

MethylomeDB

Includes genome-wide DNA methylation profiles for human and mouse brains.…

Includes genome-wide DNA methylation profiles for human and mouse brains. MethylomeDB offers an important resource for research into brain function and behavior. It provides the first source of…

DIRECTION
Desktop
P-Hint-Hunt
Algorithm

P-Hint-Hunt

Detects parallel DNA methylation. P-Hint-Hunt sacrifies a small amount of space…

Detects parallel DNA methylation. P-Hint-Hunt sacrifies a small amount of space effectiveness to in exchange for higher performance gains. It was evaluated on Tianhe-2 supercomputer. This tool…

MethHC
Dataset

MethHC

A database comprising a systematic integration of a large collection of DNA…

A database comprising a systematic integration of a large collection of DNA methylation data and mRNA/microRNA expression profiles in human cancer. MethHC integrates data such as DNA methylation,…

Epidaurus
Desktop
Web

Epidaurus

Integrative analyses of epigenetic data promise a deeper understanding of the…

Integrative analyses of epigenetic data promise a deeper understanding of the epigenome. Epidaurus is a bioinformatics tool used to effectively reveal inter-dataset relevance and differences through…

MethBank
Dataset

MethBank

A DNA methylome programming database that integrates the genome-wide…

A DNA methylome programming database that integrates the genome-wide single-base nucleotide methylomes of gametes and early embryos at multiple diverse stages in different model organisms. Unlike…

BayesMS
Desktop

BayesMS

Identifies cell-specific methylation profiles by using a Bayesian model…

Identifies cell-specific methylation profiles by using a Bayesian model selection. BayesMS determines cell-specific CpGs, the estimation of differential methylation by cell type and the assessment of…

HIMA
Desktop

HIMA High-dimensional Mediation Analysis

An R package for estimating and testing high-dimensional mediation effects in…

An R package for estimating and testing high-dimensional mediation effects in genomic/epigenomic studies. HIMA adopts the multiple mediator model’s framework and extend it to the highdimensional…

ASMBrainBlood
Dataset

ASMBrainBlood

To investigate the role of tissue-specific variation of allele-specific…

To investigate the role of tissue-specific variation of allele-specific methylation (ASM) in the human brain and its relation to allelic biases in whole blood, we examined ASM across multiple brain…

MethDB
Dataset

MethDB

The purpose of this database is to provide the scientific community with a…

The purpose of this database is to provide the scientific community with a resource to store DNA methylation data and to make these data readily available to the public.

CMS
Dataset

CMS Cancer Methylome System

A web-based database application designed for the visualization, comparison and…

A web-based database application designed for the visualization, comparison and statistical analysis of human cancer-specific DNA methylation. CMS provides visualization and analytic functions for…

A A A
Lnc2Meth
Dataset

Lnc2Meth

Informs about RNAs and DNA methylation. Lnc2Meth is an online resource that…

Informs about RNAs and DNA methylation. Lnc2Meth is an online resource that assists in comprehension of the expression of protein-coding or non-coding transcripts. Its purpose is to clarify the…

Notos
Desktop

Notos

Provides a kernel density estimation (KDE) based tool in order to estimate the…

Provides a kernel density estimation (KDE) based tool in order to estimate the level of DNA methylation. Notos is composed of two separate programs which allows to calculate the CpG o/e ratios of the…

pETM
Desktop

pETM penalized Exponential Tilt Model

Aims to combine generalized exponential tilt model with a network-based penalty…

Aims to combine generalized exponential tilt model with a network-based penalty function. pETM detects both mean and variance signals with the network-based regularization considering correlations…

Betamix
Desktop

Betamix

Represents an estimation algorithm for mixture models. Betamix rests on a…

Represents an estimation algorithm for mixture models. Betamix rests on a hybrid approach between maximum likelihood and the method of moments, and gets back the iterative framework of the EM…

H(O)TA
Desktop

H(O)TA Hairpin (Oxidative) bisulfite sequencing Time course Analyzer

Infers (hydroxy-)methylation levels and efficiencies of the involved enzymes at…

Infers (hydroxy-)methylation levels and efficiencies of the involved enzymes at a certain DNA locus. H(O)TA is based on the construction of two coupled Hidden Markov Models (HMMs). It is able to take…

iDNA4mC
Web

iDNA4mC

Provides a method for identification of DNA N4-methylcytosine (4mC) sites.…

Provides a method for identification of DNA N4-methylcytosine (4mC) sites. iDNA4mC is based on a support vector machine (SVM) in which the DNA samples are formulated by using the nucleotide chemical…

CancerLocator
Desktop

CancerLocator

Exploits the diagnostic potential of cell-free DNA by determining not only the…

Exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin…

MeDeCom
Desktop

MeDeCom

Allows the decomposition of complex DNA methylomes into latent methylation…

Allows the decomposition of complex DNA methylomes into latent methylation components and their proportions in each sample. MeDeCom is an unsupervised tool for the exploratory study of the major…

methPrimerDB
Web

methPrimerDB

This is a public database holding PCR primers for popular DNA methylation…

This is a public database holding PCR primers for popular DNA methylation analysis methods to prevent time-consuming primer design and experimental optimisation. It can design primers for two types…

PEpiD
Dataset

PEpiD Prostate Epigenetic Database

Stores the curated epigenetic data retrieved by literature mining, which…

Stores the curated epigenetic data retrieved by literature mining, which previous studies indicated as involved in prostate cancer (PC) of human, mouse, and rat. A user-friendly interface is…

EpimiR
Dataset

EpimiR

Provides a fairly comprehensive repository about the mutual regulation between…

Provides a fairly comprehensive repository about the mutual regulation between epigenetic modifications and miRNAs, which will promote the research on the regulatory mechanism of epigenetics and…

iDNA-Methyl
Web

iDNA-Methyl

Identifies DNA methylation sites via pseudo trinucleotide composition. We…

Identifies DNA methylation sites via pseudo trinucleotide composition. We anticipate that the iDNA-Methyl predictor will become a useful high-throughput tool because (i) information of DNA…

DeepMethyl
Web

DeepMethyl

A web server for predicting the DNA methylation state of CpG dinucleotide using…

A web server for predicting the DNA methylation state of CpG dinucleotide using features inferred from three-dimensional genome topology (based on Hi-C) and DNA sequence patterns. DeepMethyl is based…

LYNE
Desktop

LYNE Lineage Dynamics for Epigenetics

A Markov model framework to analyze DNA methylation dynamics across lineage…

A Markov model framework to analyze DNA methylation dynamics across lineage specifications. LYNE takes precursor to descendant relationships into account and enables inference of CpG methylation…

DBCAT
Dataset

DBCAT DataBase of CpG islands and Analytical Tool

A database developed in order to recognize comprehensive mehtylation profiles…

A database developed in order to recognize comprehensive mehtylation profiles of DNA alteration in human cancer. DBCAT is an online methylation analytical tool composed of three parts: a CpG Island…

methylInheritan…
Desktop

methylInheritance

Applies permutation-based analysis associating conserved differentially…

Applies permutation-based analysis associating conserved differentially methylated elements from one generation to the next to a treatment effect. MethylInheritance does a permutation analysis, based…

BPRMeth
Desktop

BPRMeth

Models methylation profiles and extracts higher order features. BPRMeth uses…

Models methylation profiles and extracts higher order features. BPRMeth uses the Binomial Probit Regression likelihood. The features quantitate precisely notions of shape of a methylation profile.…

REMP
Desktop

REMP Repetitive Element Methylation Prediction

Predicts DNA methylation of locus-specific repetitive elements (RE) by learning…

Predicts DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. REMP is a machine learning-based tools to provide genome wide and…

EpiFactors
Dataset

EpiFactors

A manually curated database providing information about epigenetic regulators,…

A manually curated database providing information about epigenetic regulators, their complexes, targets and products. EpiFactors contains information on 815 proteins, including 95 histones and…

CETS
Desktop

CETS Cell EpigenoType Specific

Is designed for the quantification and normalization of differing neuronal…

Is designed for the quantification and normalization of differing neuronal proportions in genome-scale DNA methylation datasets. The application of CETS quantification and transformation can reduce…

MethBase
Dataset

MethBase

A central reference methylome database created from public BS-seq datasets. It…

A central reference methylome database created from public BS-seq datasets. It contains hundreds of methylomes from well-studied organisms. For each methylome, it provides methylation level at…

DevMouse
Dataset

DevMouse

A mouse developmental methylome database which focuses on the efficient storage…

A mouse developmental methylome database which focuses on the efficient storage of DNA methylomes in temporal order and quantitative analysis of methylation dynamics during mouse development. The…

PCMdb
Dataset

PCMdb Pancreatic Cancer Methylation database

A comprehensive resource dedicated to methylation of genes in pancreatic cancer.

A comprehensive resource dedicated to methylation of genes in pancreatic cancer.

MENT
Dataset

MENT Methylation and Expression database of Normal and Tumor tissues

Provides a multicentre prostate cancer database that captures clinicopathologic…

Provides a multicentre prostate cancer database that captures clinicopathologic data and longitudinal follow-up. CPDR is a research program for studying prostate diseases. It is divided into: (1) a…

Kineticstools
Desktop

Kineticstools

Detects DNA modifications from single molecule. Kineticstools can be used in…

Detects DNA modifications from single molecule. Kineticstools can be used in real-time sequencing data. It makes independent comparison of IPDs at each position on the genome, for each strand, and…

HDMFinder
Desktop

HDMFinder

Implements a computational pattern recognition method that is used to predict…

Implements a computational pattern recognition method that is used to predict the methylation landscape of human brain DNA. HDMFinder method can be applied both to CpG islands and to non-CpG island…

NCBI…
Dataset

NCBI Epigenomics

Explore, view, and download genome-wide maps of DNA and histone modifications…

Explore, view, and download genome-wide maps of DNA and histone modifications from our diverse collection of epigenomic data sets. The Epigenomics resource also provides the user with a unique…

DDMGD
Dataset

DDMGD Dragon Database for Methylated Genes and Diseases

Provides a comprehensive repository of information related to genes methylated…

Provides a comprehensive repository of information related to genes methylated in diseases that can be found through text mining. DDMGD's scope is not limited to a particular group of genes,…

MethmiRbase
Dataset

MethmiRbase

A database that makes use of meta-analysis to identify potential…

A database that makes use of meta-analysis to identify potential epigenetic-regulated miRNAs for three human cancers, i.e. lung adenocarcinoma, lung squamous carcinoma and ovarian cancers.…

MeInfoText
Web

MeInfoText

A web server that can provide gene methylation and cancers associations based…

A web server that can provide gene methylation and cancers associations based on text-mining and maximum entropy.

MethCGI
Web

MethCGI

A classifier for predicting methylation status of CpG islands using a support…

A classifier for predicting methylation status of CpG islands using a support vector machine (SVM). Nucleotide sequence contents as well as transcription factor binding sites (TFBSs) are used as…

Methylator
Web

Methylator

A support vector machine (SVM)-based method for the prediction of cytosine…

A support vector machine (SVM)-based method for the prediction of cytosine methylation in CpG dinucleotides. Initially a SVM module was developed from human data for the prediction of human-specific…

CGPredictor
Desktop

CGPredictor Cancer Grade Predictor

Localizes and examines biomarkers from strong self-similarity pattern on…

Localizes and examines biomarkers from strong self-similarity pattern on patients’ profiles. CGPredictor can facilitate the identification of distinct phenotypes in a variety of cancers. It…

Information

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