While some software tools to analyze and visually represent DNA methylation data have been published (reviewed in Laird, 2010), its use by wet lab users is often limited. On the other hand, popular spreadsheet tools like Excel are unable to generate lollipop plots by default.…
Desktop app
G T A T C G C T A Genome Bisulfite… Genome Bisulfite Sequencing Analyser

GBSA Genome Bisulfite Sequencing Analyser

An open-source software tool capable of analysing whole-genome bisulfite…

An open-source software tool capable of analysing whole-genome bisulfite sequencing data with either a gene-centric or gene-independent focus. GBSA’s output can be easily integrated with other…

Web app
G T A T C G C T A WashU Epigenome… WashU Epigenome Browser

WashU Epigenome Browser

A genome browser focusing on the human epigenome. The Browser is web-based and…

A genome browser focusing on the human epigenome. The Browser is web-based and it extends the seminal concept invented by the UCSC Cancer Genomics Browser to support large, sequencing-based datasets.…

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 BigWig/BigBed BigWig/BigBed

BigWig/BigBed

Allow the high-performance display of next-generation sequencing experiment…

Allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser.

Desktop app
G T A T C G C T A MethylViewer MethylViewer

MethylViewer

Interactive data analysis of bisulphite DNA sequencing to map chromatin…

Interactive data analysis of bisulphite DNA sequencing to map chromatin structure using DNA methyltransferases.

Desktop app
G T A T C G C T A HilbertVis HilbertVis

HilbertVis

This tool allows to display very long data vectors in a space-efficient manner,…

This tool allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaneously with the…

Desktop app
G T A T C G C T A DNA Methylation… DNA Methylation Entropy Analysis Software

DMEAS DNA Methylation Entropy Analysis Software

Analyzes the distribution of DNA methylation patterns for the quantification of…

Analyzes the distribution of DNA methylation patterns for the quantification of epigenetic heterogeneity. DMEAS supports the analysis of both locus-specific and genome-wide bisulfite sequencing data.…

Desktop app
G T A T C G C T A methVisual methVisual

methVisual

Enables exploratory analysis and intuitive visualization of DNA methylation…

Enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. MethVisual allows the import of DNA methylation sequences, aligns…

Desktop app
G T A T C G C T A CpGviewer CpGviewer

CpGviewer

Aims to be a simple integrated tool for handling bisulphite sequencing…

Aims to be a simple integrated tool for handling bisulphite sequencing projects. CpGviewer can process plain text sequences or a variety of electropherogram formats, and allows interactive editing of…

Web app
G T A T C G C T A Methylation plotter Methylation plotter

Methylation plotter

A Web tool that allows the visualization of methylation data in a user-friendly…

A Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality.

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 ViewBS ViewBS

ViewBS

Explores and visualizes bisulfite sequencing (BS-seq) data. ViewBS has several…

Explores and visualizes bisulfite sequencing (BS-seq) data. ViewBS has several top level commands which determine the required and optimal arguments. These commands can be divided into two parts:…

Desktop app
Web app
G T A T C G C T A Methylmapper Methylmapper

Methylmapper

Generates cluster plots from the results of high-throughput methylation…

Generates cluster plots from the results of high-throughput methylation analysis through bisulfite sequencing.

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 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
G T A T C G C T A MethTools MethTools

MethTools

A collection of software tools for the handling and analysis of DNA methylation…

A collection of software tools for the handling and analysis of DNA methylation data generated by the Bisulfite Genomic Sequencing method.

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 MochiView MochiView

MochiView

Java software that integrates browsing of genomic sequences, features, and data…

Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis.

Desktop app
G T A T C G C T A iMethy iMethy

iMethy

For investigation and visualization of DNA methylation by high-throughput…

For investigation and visualization of DNA methylation by high-throughput bisulfite sequencing.

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…

G T A T C G C T A methylation profiles… Deprecated methylation profiles of DNA

mPod methylation profiles of DNA

A resource for human genome-wide tissue-specific DNA methylation profiles. mPod…

A resource for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues,…

Web app
G T A T C G C T A Methylyzer Methylyzer

Methylyzer

Represents DNA methylation data obtained from bisulfite genomic sequencing.…

Represents DNA methylation data obtained from bisulfite genomic sequencing. Graphical representation of the data includes the methylation status of single CpG dinucleotides. Mutations (replacements,…

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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