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Chromatin-state detection and characterization software tools | Epigenomics

Readout of genetic information in eukaryotic genomes is mediated by the dynamic chromatin environment, which regulates DNA accessibility for the gene expression machinery through chromatin compaction, associated histone modifications and…
G T A T C G C T A
ChromHMM
Desktop

ChromHMM

A software program for learning and characterizing chromatin states. ChromHMM…

A software program for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the…

Spectacle
Desktop

Spectacle Spectral learning for Annotating Chromatin Labels and Epigenomes

Annotates chromatin states in the genome from epigenome maps. Spectacle is a…

Annotates chromatin states in the genome from epigenome maps. Spectacle is a software which implements a spectral learning algorithm for hidden Markov models (HMM) for epigenomic data. It extends…

G T A T C G C T A
Segway
Desktop

Segway

Contains a method for analyzing multiple tracks of functional genomics data.…

Contains a method for analyzing multiple tracks of functional genomics data. Segway uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even…

StatePaintR
Desktop

StatePaintR

Facilitates the use of StateHub models to generate browser tracks for…

Facilitates the use of StateHub models to generate browser tracks for bioinformatic analyses. StatePaintR is a software package which translates epigenomics files into segmentations using these…

CMINT
Desktop

CMINT Chromatin Module INference on Trees

Identifies chromatin modules in multiple cell types simultaneously. CMINT is a…

Identifies chromatin modules in multiple cell types simultaneously. CMINT is a generative probabilistic graphical model-based approach for multitask clustering. It was developed to enable systematic…

PCSD
Dataset

PCSD plant chromatin state database

Contains search tools, analysis tools and the UCSC Genome Browser for…

Contains search tools, analysis tools and the UCSC Genome Browser for visualization. PCSD is a plant chromatin state database to integrate information on chromatin states, self-organization mapping…

StateHub
Dataset

StateHub

Stores chromatin state definition tables to paint the genome with functional…

Stores chromatin state definition tables to paint the genome with functional annotation. StateHub is a database which hosts annotation tracks for major public consortia as a resource, and allows…

hiHMM
Desktop

hiHMM hierarchically-linked infinite Hidden Markov Model

A Bayesian non-parametric method to jointly infer chromatin state maps in…

A Bayesian non-parametric method to jointly infer chromatin state maps in multiple genomes (different species, cell types, and developmental stages) using genome-wide histone modification data. This…

tree-hmm
Desktop

tree-hmm

A Bayesian network that uses epigenetic modifications to simultaneously model…

A Bayesian network that uses epigenetic modifications to simultaneously model 1) chromatin mark combinations that give rise to different chromatin states and 2) propensities for transitions between…

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