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 various temporal and spatial…
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…

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

An algorithm to analyze single-nucleotide resolution methylation data.

An algorithm to analyze single-nucleotide resolution methylation data.

G T A T C G C T A
BiSeq
Desktop

BiSeq

The package provides useful classes and functions to handle and analyze…

The package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data.

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
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

It provides a quantitative approach to quantify methylation difference and…

It provides a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy.

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
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

A streamlined package to meet the need of extracting multiple types of…

A streamlined package to meet the need of extracting multiple types of information (such as differentially methylated C sites (DMCs), differentially methylated regions (DMRs), single nucleotide…

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
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
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
bsseq
Desktop

bsseq

A package for analyzing, managing and storing bisulfite sequencing data.

A package for analyzing, managing and storing bisulfite sequencing data.

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
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.