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

Most recent bioinformatics tools

plot2DO
Desktop

plot2DO Plot 2D Occupancies

Allows users to plot the 2D occupancy (2DO) of genomic data. plot2DO allows the…

Allows users to plot the 2D occupancy (2DO) of genomic data. plot2DO allows the investigation of paired-end sequencing data originating from a variety of organisms. It assists user in creation of 2D…

dCMA
Desktop

dCMA differential Chromatin Modification Analysis

Identifies cell-type-specific regulatory elements (CSREs) in the human genome.…

Identifies cell-type-specific regulatory elements (CSREs) in the human genome. dCMA is a computational framework capable of identifying genomic regions, containing distinctive chromatin modifications…

P-Hint-Hunt
Algorithm

P-Hint-Hunt

Detects parallel DNA methylation. P-Hint-Hunt sacrifies a small amount of space…

Detects parallel DNA methylation. P-Hint-Hunt sacrifies a small amount of space effectiveness to in exchange for higher performance gains. It was evaluated on Tianhe-2 supercomputer. This tool…

CR2Cancer
Dataset

CR2Cancer

Gathers information about chromatin regulators (CRs) in human cancer. CR2Cancer…

Gathers information about chromatin regulators (CRs) in human cancer. CR2Cancer is a database that allows users to explore the functional, genomic, transcriptomic, proteomic, clinical, biological…

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.…

Curators for Epigenomics

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