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…
Desktop app
G T A T C G C T A methylKit methylKit

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…

Desktop app
G T A T C G C T A Bisulfighter Bisulfighter

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.

Desktop app
G T A T C G C T A City of Hope CpG… City of Hope CpG Island Analysis Pipeline

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.

Desktop app
G T A T C G C T A BiSeq BiSeq

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.

Desktop app
G T A T C G C T A MethPipe MethPipe

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…

Desktop app
G T A T C G C T A eDMR eDMR

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.

Desktop app
G T A T C G C T A combined-pvalues combined-pvalues

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…

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

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…

Desktop app
G T A T C G C T A metilene metilene

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…

Desktop app
G T A T C G C T A DMAP DMAP

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…

Desktop app
G T A T C G C T A GetisDMR GetisDMR

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…

Desktop app
G T A T C G C T A Streamlined… Streamlined Methylation Analysis Pipeline

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…

Desktop app
G T A T C G C T A MethylPurify MethylPurify

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…

Desktop app
G T A T C G C T A Regression Analysis… Regression Analysis of Differential Methylation

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…

Desktop app
G T A T C G C T A M3D M3D

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…

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

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…

Desktop app
Web app
G T A T C G C T A Web Service for… Web Service for Bisulfite Sequencing Data Analysis

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…

Desktop app
G T A T C G C T A methylSig methylSig

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.

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

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…

Desktop app
G T A T C G C T A methylMnM methylMnM

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.

Desktop app
G T A T C G C T A bsseq bsseq

bsseq

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

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

Desktop app
G T A T C G C T A dmrFinder dmrFinder

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,…

Desktop app
G T A T C G C T A Qvalue Qvalue

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…

Desktop app
G T A T C G C T A swDMR swDMR

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.

Desktop app
G T A T C G C T A QDMR QDMR

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.

Desktop app
G T A T C G C T A CpG_MPs CpG_MPs

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…

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

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…

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