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Epigenomic analysis software tools and databases

For didactic purposes, epigenetic modifications can be grouped into three main categories: DNA methylation, histone modifications and nucleosome positioning (Portela and Esteller, 2010). An altered pattern of epigenetic modifications is central to many common human diseases,…

Epigenomics steps

Experts in Epigenomics

They share and annotate bioinformatics tools

Most recent bioinformatics tools

MethFinder
Desktop

MethFinder

Offers a method for detecting tissue-specific methylation patterns. MethFinder…

Offers a method for detecting tissue-specific methylation patterns. MethFinder provides a classifier able to identify patterns through tissues and compute DNA methylation levels. The application is…

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EPITRANS
Dataset

EPITRANS

Represents relationships between gene expression and epigenetic modifications.…

Represents relationships between gene expression and epigenetic modifications. EPITRANS provides about 360 microarrays and 280 Next Generation Sequencing (NGS) data sets for 28 human tissues. It…

Epigenomics in…
Desktop

Epigenomics in JBrowse

Allows visualization of specialized sequencing data in epigenomics. Epigenomics…

Allows visualization of specialized sequencing data in epigenomics. Epigenomics in JBrowse is a collection of plugins designed for JBrowe. It includes visualizing base modifications and small RNAs as…

HebbPlot
Desktop

HebbPlot

Produces a pattern representing mark distributions around all of the regions.…

Produces a pattern representing mark distributions around all of the regions. HebbPlot uses a Hebb network to learn how a mark is distributed around a set of regions that have the same function. It…

Most popular analytical software and databases

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)…

BS Seeker
Desktop

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…

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…

iNuc-STNC
Desktop

iNuc-STNC

Allows users to identify nucleosome positioning in genomes. iNuc-STNC utilizes…

Allows users to identify nucleosome positioning in genomes. iNuc-STNC utilizes various extraction techniques to find and extract salient and nominal features from nucleosome positioning sequences.…

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