Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Chromatin segmentation software tools | ChIP sequencing data analysis

The segmentation of epigenomes into chromatin states collapses the ChIP-seq tracks and provides an abstract view on the multi-dimensional data. A chromatin state is a recurrent pattern in the abundances of a given set of histone modifications,…
G T A T C G C T A
ChromImpute
Desktop

ChromImpute

A software tool for large-scale systematic epigenome imputation. ChromImpute…

A software tool for large-scale systematic epigenome imputation. ChromImpute takes an existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not…

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…

G T A T C G C T A
PARE
Web
Desktop

PARE Predict Active Regulatory Elements

A computational method that systematically analyzes the H3K4me1 or H3K4me3…

A computational method that systematically analyzes the H3K4me1 or H3K4me3 peak-valley-peak (PVP) patterns to predict nucleosome free regions (NFRs). We show that NFRs predicted by H3K4me1 and me3…

G T A T C G C T A
EpiCSeg
Desktop

EpiCSeg Epigenome Count-based Segmentation

Combines several histone modification maps for the segmentation and…

Combines several histone modification maps for the segmentation and characterization of cell-type specific epigenomic landscapes. By using an accurate probabilistic model for the read counts, EpiCSeg…

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…

G T A T C G C T A
START
Dataset

START Signal Track Analytical Research Tool

Allows simple integrated analysis of private and commonly-used public signal…

Allows simple integrated analysis of private and commonly-used public signal tracks. START provides a simple and generic way for analyzing a large number of genomic signal tracks. This database…

G T A T C G C T A
GenoSTAN
Desktop

GenoSTAN Genomic STate ANnotation

A method for de novo and unbiased inference of chromatin states from…

A method for de novo and unbiased inference of chromatin states from genome-wide profiling data. In contrast to previously described methods for chromatin state annotation, GenoSTAN directly models…

G T A T C G C T A
DNN-HMM
Desktop

DNN-HMM

A hybrid architecture combining a pre-trained, deep neural network and a hidden…

A hybrid architecture combining a pre-trained, deep neural network and a hidden Markov model (DNN-HMM) for the de novo identification of replication domains using replication timing profiles. Our…

G T A T C G C T A
ChromBiSim
Desktop

ChromBiSim CHROMatin BIclustering SIMplified

Allows to calculate biclusters. ChromBiSim is based on binarized data matrix of…

Allows to calculate biclusters. ChromBiSim is based on binarized data matrix of gene expression data sets. It can run on any size of data including whole genome histone modification profiles…

iSeg
Desktop

iSeg

Permits user to work on segmentation of genomic and epigenomic profiles. iSeg…

Permits user to work on segmentation of genomic and epigenomic profiles. iSeg uses both simulated and experimental data and can detect segments of any length. Moreover, it can detect candidate…

G T A T C G C T A
CHROMATRA
Desktop

CHROMATRA CHROmatin Mapping Across TRAnscripts

Provides a visualization tool available as plug-in for the Galaxy platform.…

Provides a visualization tool available as plug-in for the Galaxy platform. CHROMATRA allows detailed yet concise presentations of data derived from ChIP-chip or ChIP-seq experiments by visualizing…

G T A T C G C T A
epicode
Desktop

epicode

A non-negative matrix factorization method to discover combinatorial patterns…

A non-negative matrix factorization method to discover combinatorial patterns of epigenetic marks that frequently co-occur in subsets of genomic regions. epicope discovers patterns of histone…

G T A T C G C T A
EMdeCODE
Desktop

EMdeCODE

An original algorithm that approximate the genomic distribution of given DNA…

An original algorithm that approximate the genomic distribution of given DNA features (e.g. promoter, enhancer, viral integration) by identifying relevant ChIPSeq profiles of post-translational…

G T A T C G C T A
ChromaSig
Desktop

ChromaSig

An unsupervised learning method to find, in an unbiased fashion, commonly…

An unsupervised learning method to find, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data. ChromaSig recovers known patterns associated…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.