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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…
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.…

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…

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…

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…

Cscan
Web

Cscan

A web resource that includes a large collection of genome-wide ChIP-Seq…

A web resource that includes a large collection of genome-wide ChIP-Seq experiments performed on TFs, histone modifications, RNA polymerases and others.

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