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

Differentially methylated region detection software tools | Bisulfite sequencing data analysis

DNA methylation plays critical roles in transcriptional regulation and chromatin remodeling. Differentially methylated regions (DMRs) have important implications for development, aging and diseases. Therefore, genome-wide mapping of DMRs across…
G T A T C G C T A
SMART
Desktop

SMART Specific Methylation Analysis and Report Tool

Detects the cell type-specific methylation marks by integrating multiple…

Detects the cell type-specific methylation marks by integrating multiple methylomes from human cell lines and tissues. SMART is an entropy-based framework focused on integrating of a large number of…

G T A T C G C T A
DSS-single
Desktop

DSS-single

A package based on a statistical method for detecting DMRs from WGBS (Whole…

A package based on a statistical method for detecting DMRs from WGBS (Whole Genome Bisulfite Sequencing) data without replicates. A key feature of DSS-single is to estimate biological variation when…

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),…

G T A T C G C T A
methylKit
Desktop

methylKit

An R package for DNA methylation analysis and annotation from high-throughput…

An R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. methylKit is designed to deal with sequencing data from RRBS and its variants, but also…

G T A T C G C T A
metilene
Desktop

metilene

Identifies differentially methylated regions (DMRs) within whole genome and…

Identifies differentially methylated regions (DMRs) within whole genome and targeted sequencing data with unrivaled specificity and sensitivity. A binary segmentation algorithm combined with a…

G T A T C G C T A
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.…

G T A T C G C T A
BiSeq
Desktop

BiSeq

Provides useful classes and functions to handle and analyze targeted bisulfite…

Provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, BiSeq implements an…

G T A T C G C T A
ABBA
Desktop

ABBA Approximate Bayesian Bisulphite sequencing Analysis

Creates a smoothed methylation profile from sets of methylated/unmethylated…

Creates a smoothed methylation profile from sets of methylated/unmethylated reads from whole genome bi-sulphite sequencing, extracting significantly differentially methylated regions. ABBA is a…

G T A T C G C T A
MACAU
Desktop

MACAU Mixed model Association for Count data via data Augmentation

Allows to simultaneously account for both the over-dispersed, count-based…

Allows to simultaneously account for both the over-dispersed, count-based nature of bisulfite sequencing data, as well as genetic relatedness among individuals. MACAU is a binomial mixed model and an…

G T A T C G C T A
Bisulfighter
Desktop

Bisulfighter

A software package for detecting methylated cytosines (mCs) and differentially…

A software package for detecting methylated cytosines (mCs) and differentially methylated regions (DMRs) from bisulfite sequencing data.

G T A T C G C T A
DSS-general
Desktop

DSS-general

A statistical method to detect differentially methylated loci (DML) for BS-seq…

A statistical method to detect differentially methylated loci (DML) for BS-seq data under general experimental design. At each CpG site, the count data are modeled by a beta-binomial regression with…

G T A T C G C T A
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…

G T A T C G C T A
DMAP
Desktop

DMAP

A fragment-based approach for investigating DNA methylation patterns for…

A fragment-based approach for investigating DNA methylation patterns for reduced representation bisulphite sequencing data. DMAP can directly import the output from any bisulphite aligner in sequence…

G T A T C G C T A
eDMR
Desktop

eDMR

Comprehensive DMR analysis based on bimodal normal distribution model and…

Comprehensive DMR analysis based on bimodal normal distribution model and weighted cost function for regional methylation analysis optimization.

G T A T C G C T A
CpG_MPs
Desktop

CpG_MPs

A comprehensive tool for identification and analysis of the methylation…

A comprehensive tool for identification and analysis of the methylation patterns of genomic regions from bisulfite sequencing data. CpG_MPs first normalizes bisulfite sequencing reads into…

G T A T C G C T A
bicycle
Desktop

bicycle BIsulfite-based methylCYtosine CalLEr

Analyzes whole genome bisulfite sequencing (WGBS) data. bicycle is a…

Analyzes whole genome bisulfite sequencing (WGBS) data. bicycle is a next-generation sequencing (NGS) bioinformatic pipeline that can process data from directional (Lister) and non-directional…

G T A T C G C T A
M3D
Desktop

M3D

A non-parametric, kernel-based method, M3D, to detect higher order changes in…

A non-parametric, kernel-based method, M3D, to detect higher order changes in methylation profiles, such as shape, across pre-defined regions. The test statistic explicitly accounts for differences…

G T A T C G C T A
HMM-DM
Desktop

HMM-DM

Detects differentially methylated (DM) regions from bisulfite sequencing (BS)…

Detects differentially methylated (DM) regions from bisulfite sequencing (BS) data generated from different protocols, such as whole-genome bisulfite sequencing (WGBS) and reduced representative BS.…

G T A T C G C T A
MethPipe
Desktop

MethPipe

A computational pipeline for analyzing bisulfite sequencing data (WGBS and…

A computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS). MethPipe is a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of…

G T A T C G C T A
GetisDMR
Desktop

GetisDMR

A statistical method to detect differentially methylated regions (DMRs) from…

A statistical method to detect differentially methylated regions (DMRs) from whole-genome bisulfite sequencing (WGBS) datasets. GetisDMR utilizes the beta-binomial regression model to account for…

G T A T C G C T A
MethylPurify
Desktop

MethylPurify

Uses regions with bisulfite reads showing discordant methylation levels to…

Uses regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples alone. MethylPurify can identify differentially methylated regions (DMRs) from…

G T A T C G C T A
SMAP
Desktop

SMAP Streamlined Methylation Analysis Pipeline

Allows to extract multiple types of information (such as DMCs, DMRs, SNPs and…

Allows to extract multiple types of information (such as DMCs, DMRs, SNPs and ASM) from various types of RRBS and Bis-seq data. SMAP is designed to be an easy-to-use, one-stop and sophisticated…

G T A T C G C T A
HOME
Desktop

HOME Histogram Of MEthylation

Consists in a differentially methylated region (DMR) finder taking into account…

Consists in a differentially methylated region (DMR) finder taking into account important characteristics such as cytosine spatial correlation, sequencing depth, and biological variation between…

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…

G T A T C G C T A
dmrseq
Desktop

dmrseq

Detects candidate regions and evaluates statistical significance at the region…

Detects candidate regions and evaluates statistical significance at the region level. dmrseq is a two-stage approach that calculates a statistic for each candidate differentially methylated region…

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…

G T A T C G C T A
HMM-Fisher
Desktop

HMM-Fisher

Identifies differentially methylated cytosines and regions. Hidden Markov model…

Identifies differentially methylated cytosines and regions. Hidden Markov model (HMM)-Fisher is efficient and robust in identifying heterogeneous differentially methylated (DM) regions. This method…

G T A T C G C T A
methylSig
Desktop

methylSig

R package for analyzing whole-genome bisulfite sequencing (bis-seq), reduced…

R package for analyzing whole-genome bisulfite sequencing (bis-seq), reduced representation bisulfite sequencing (RRBS), or enhanced RRBS experiments.

G T A T C G C T A
Methy-Pipe
Desktop

Methy-Pipe

A software tool that not only fulfills the core data analysis requirements…

A software tool that not only fulfills the core data analysis requirements (e.g. sequence alignment, differential methylation analysis, etc.) but also provides useful tools for methylation data…

G T A T C G C T A
WBSA
Desktop
Web

WBSA Web Service for Bisulfite Sequencing Data Analysis

A free web application for analysis of whole-genome bisulfite-sequencing (WGBS)…

A free web application for analysis of whole-genome bisulfite-sequencing (WGBS) and genome-wide reduced representation bisulfite sequencing (RRBS) data. WBSA not only focuses on CpG methylation, but…

G T A T C G C T A
DMRcaller
Desktop

DMRcaller

Recognizes differentially methylated regions between the conditions in CG and…

Recognizes differentially methylated regions between the conditions in CG and non-CG context. DMRcaller utilizes bisulfite sequencing data in two conditions to proceed. It is able to extract from the…

G T A T C G C T A
methylMnM
Desktop

methylMnM

To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for…

To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison.

G T A T C G C T A
dmrFinder
Desktop

dmrFinder

A package that implements analysis tools for DNA methylation data generated…

A package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. dmrFinder finds differentially methylated regions between samples,…

G T A T C G C T A
Qvalue
Desktop

Qvalue

Takes a list of p-values resulting from the simultaneous testing of many…

Takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives…

G T A T C G C T A
swDMR
Desktop

swDMR

A free software using a sliding-window approach to identify differentially…

A free software using a sliding-window approach to identify differentially methylated regions (DMR) from whole-genome bisulfite sequencing.

G T A T C G C T A
RADMeth
Desktop

RADMeth Regression Analysis of Differential Methylation

A software package for computing individual differentially methylated sites and…

A software package for computing individual differentially methylated sites and genomic regions in whole genome bisulfite sequencing (WGBS) data. For rapid differential methylation analysis, RADMeth…

G T A T C G C T A
SCREW
Desktop

SCREW Single Cell Reproducible Epigenomics Workflow

Performs standard single-cell DNA methylation analyses. SCREW consists in…

Performs standard single-cell DNA methylation analyses. SCREW consists in several Common Workflow Language (CWL)+Dockerised tools, as well as mini and complete templates workflows.

G T A T C G C T A
RRBS-Analyser
Web

RRBS-Analyser

A comprehensive genome-scale DNA methylation analysis server based on RRBS…

A comprehensive genome-scale DNA methylation analysis server based on RRBS data. RRBS-Analyser can assess sequencing quality, generate detailed statistical information, align the bisulfite-treated…

Information

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