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Histone modification tools

Histone modifications play important roles in chromatin remodeling, gene transcriptional regulation, stem cell maintenance and differentiation. Alterations in histone modifications may be linked to human diseases especially cancer. Histone…
modENCODE
Dataset

modENCODE

Provides the biological research community with a comprehensive encyclopedia of…

Provides the biological research community with a comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research…

Epigram
Desktop

Epigram

Predicts histone modification and DNA methylation patterns from DNA motifs.…

Predicts histone modification and DNA methylation patterns from DNA motifs. Epigram is an analysis pipeline used to systematically identify DNA motifs that are predictive of epigenomic modifications.…

WERAM
Dataset

WERAM Writers Erasers and Readers of Acetylation and Methylation

A database for histone acetyltransferases, histone deacetylases, histone…

A database for histone acetyltransferases, histone deacetylases, histone methyltransferases, histone demethylases and acetyl- or methyl-binding proteins, which catalyze, remove and recognize histone…

HIstome
Dataset

HIstome

A database of human histones, their post-translational modifications and…

A database of human histones, their post-translational modifications and modifying enzymes. The database covers 5 types of histones, 8 types of their post-translational modifications and 13 classes…

HistoneHits
Dataset

HistoneHits

A database for histone mutations and their phenotypes. The database collects…

A database for histone mutations and their phenotypes. The database collects phenotypic screening data from assays of systematically constructed histone mutants: Single-residue substitutions,…

HistoneDB
Dataset

HistoneDB

Holds canonical histones and histone variants, their sequence, structural and…

Holds canonical histones and histone variants, their sequence, structural and functional features. HistoneDB is composed of two distinct parts: the first is a set of manually curated and annotated…

DeepChrome
Web
Desktop

DeepChrome

Handles all the bins together, capturing both neighboring range and long range…

Handles all the bins together, capturing both neighboring range and long range interactions among input features, as well as automatically extract important features. DeepChrome is a unified…

GED
Dataset

GED Gametogenesis Epigenetic modification Database

A comprehensive resource of epigenetic modification of gametogenesis. Users can…

A comprehensive resource of epigenetic modification of gametogenesis. Users can get the information about epigenetic modifications (DNA methylation, histone modification and miRNA regulation) and the…

HHMD
Dataset

HHMD Human Histone Modification Database

A relatively comprehensive database for human histone modifications. HHMD…

A relatively comprehensive database for human histone modifications. HHMD focuses on the storage and integration of histone modification datasets that were obtained from laboratory experiments. HHMD…

THOR
Desktop

THOR

An HMM-based approach to detect and analyze differential peaks in two sets of…

An HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, normalization…

SUPERmerge
Desktop

SUPERmerge

Allows the analysis and annotation of coverage islands within individual read…

Allows the analysis and annotation of coverage islands within individual read alignment (BAM) files of histone modification ChIPseq datasets harboring broad chromatin domains. SUPERmerge allows…

Epidaurus
Desktop
Web

Epidaurus

Integrative analyses of epigenetic data promise a deeper understanding of the…

Integrative analyses of epigenetic data promise a deeper understanding of the epigenome. Epidaurus is a bioinformatics tool used to effectively reveal inter-dataset relevance and differences through…

geneXtendeR
Desktop

geneXtendeR

An R/Bioconductor package for histone modification ChIP-seq analysis.…

An R/Bioconductor package for histone modification ChIP-seq analysis. geneXtendeR is designed to optimally annotate a histone modification ChIP-seq peak input file with functionally important genomic…

MUSIC
Desktop

MUSIC MUltiScale EnrIchment Calling

A tool for identification of enriched regions at multiple length scales that…

A tool for identification of enriched regions at multiple length scales that the user can select, using the data from ChIP-Seq experiments. MUSIC performs favorably in terms of accuracy and…

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…

PEpiD
Dataset

PEpiD Prostate Epigenetic Database

Stores the curated epigenetic data retrieved by literature mining, which…

Stores the curated epigenetic data retrieved by literature mining, which previous studies indicated as involved in prostate cancer (PC) of human, mouse, and rat. A user-friendly interface is…

dbHiMo
Dataset

dbHiMo

A web-based genomics platform for histone-modifying enzymes (HMEs) by using HMM…

A web-based genomics platform for histone-modifying enzymes (HMEs) by using HMM sequence profiles. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting…

EpiRegNet
Web

EpiRegNet

A tool to build a transcriptional regulatory network composing of histone…

A tool to build a transcriptional regulatory network composing of histone modification and transcription factor binding in promoters and interactions between factors in these two fields. Given a set…

NCBI…
Dataset

NCBI Epigenomics

Explore, view, and download genome-wide maps of DNA and histone modifications…

Explore, view, and download genome-wide maps of DNA and histone modifications from our diverse collection of epigenomic data sets. The Epigenomics resource also provides the user with a unique…

iHMS
Dataset

iHMS

Enables comprehensive query and comparative analysis based on gene names,…

Enables comprehensive query and comparative analysis based on gene names, genomic region locations, histone modification marks and cell types. iHMS is an integrated human histone modification…

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