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Nucleosome positioning software tools | ChIP sequencing data analysis

Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning…
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F-Seq
Desktop

F-Seq

A software package that generates a continuous tag sequence density estimation…

A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome…

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TemplateFilter
Desktop

TemplateFilter

High-Resolution Nucleosome Mapping Reveals Transcription-Dependent Promoter…

High-Resolution Nucleosome Mapping Reveals Transcription-Dependent Promoter Packaging.

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DANPOS
Desktop

DANPOS Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing

A comprehensive bioinformatics pipeline explicitly designed for dynamic…

A comprehensive bioinformatics pipeline explicitly designed for dynamic nucleosome analysis at single-nucleotide resolution. DANPOS is also robust in defining functional dynamic nucleosomes, not only…

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BINOCh
Desktop

BINOCh

A package that allows biologists to carry out an analysis of nucleosome…

A package that allows biologists to carry out an analysis of nucleosome occupancy data to discover stimulus-induced transcription factor binding. BINOCh first uses histone-related ChIP-seq data to…

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PING
Desktop

PING

A flexible and powerful open-source package for nucleosome positioning using…

A flexible and powerful open-source package for nucleosome positioning using MNase-Seq data or MNase– or sonicated– ChIP-Seq data combined with either single-end (SE) or paired-end (PE)…

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ChIPseqR
Desktop

ChIPseqR

A package based on an algorithm for the analysis of nucleosome positioning and…

A package based on an algorithm for the analysis of nucleosome positioning and histone modification ChIP-seq experiments. ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome…

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NUCwave
Desktop

NUCwave

A bioinformatic tool that generates nucleosome occupation maps from chromatin…

A bioinformatic tool that generates nucleosome occupation maps from chromatin digestion with micrococcal nuclease (MNase-seq), chemical cleavage (CC-seq), chromatin inmunoprecipitation (ChIP-seq) and…

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NucPosSimulator
Desktop

NucPosSimulator

A simulation tool to identify positions of nucleosomes from Next Generation…

A simulation tool to identify positions of nucleosomes from Next Generation Sequencing data.

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NucHunter
Desktop

NucHunter

Inferring nucleosome positions with their histone mark annotation from ChIP…

Inferring nucleosome positions with their histone mark annotation from ChIP data.

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DiNuP
Desktop

DiNuP

A Systematic Approach to Identify Regions of Differential Nucleosome…

A Systematic Approach to Identify Regions of Differential Nucleosome Positioning.

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NucTools
Desktop

NucTools

Allows calculations of nucleosome occupancy profiles averaged over several…

Allows calculations of nucleosome occupancy profiles averaged over several replicates, comparisons of nucleosome occupancy landscapes between different experimental conditions, and the estimation of…

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Dimnp
Desktop

Dimnp

Identifies differential nucleosome regions (DNRs) in multiple samples. Dimnp is…

Identifies differential nucleosome regions (DNRs) in multiple samples. Dimnp is able to identify all the DNRs that are identified by two-sample method Danpos. It shows a good capacity (area under the…

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ArchAlign
Desktop

ArchAlign

A chromatin architecture alignment algorithm. ArchAlign identifies shared…

A chromatin architecture alignment algorithm. ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets derived from next-generation sequencing or…

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SANEFALCON
Desktop

SANEFALCON Single reAds Nucleosome-basEd FetAL fraCtiON

A tool developped for calculate the fetal fraction for noninvasive prenatal…

A tool developped for calculate the fetal fraction for noninvasive prenatal testing based on genome-wide nucleosome profiles, based on single end sequencing of cell-free DNA. We found a difference…

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NucDe
Desktop

NucDe

An R package mapping nucleosome-linker boundaries from both MNase-Chip and…

An R package mapping nucleosome-linker boundaries from both MNase-Chip and MNase-Seq data using a non-homogeneous hidden-state model based on first order differences of experimental data along…

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Nu-OSCAR
Web

Nu-OSCAR Nucleosome-Occupancy Study for Cis-elments Accurate Recognition

A program that can be used to identify binding sites of known transcription…

A program that can be used to identify binding sites of known transcription factors, which further incorporates nucleosome occupancy around sites on promoter regions, thereby improving the accuracy…

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NSeq
Desktop

NSeq

A multithreaded Java application for finding positioned nucleosomes from…

A multithreaded Java application for finding positioned nucleosomes from sequencing data.

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ArchTEx
Desktop

ArchTEx Architectural Tag Extender

The extension of mapped sequence tags is a common step in the analysis of…

The extension of mapped sequence tags is a common step in the analysis of single-end next-generation sequencing (NGS) data from protein localization and chromatin studies. The optimal extension can…

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PuFFIN
Desktop

PuFFIN Positioning for Fuzzy and FIxed Nucleosomes

Builds genome-wide nucleosome maps specifically designed to take advantage of…

Builds genome-wide nucleosome maps specifically designed to take advantage of paired-end reads. PuFFIN is a method to produce a higher number of detected nucleosomes. In contrast to other approaches…

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NPS
Desktop

NPS Nucleosome Positioning from Sequencing

A python software package that can identify nucleosome positions given…

A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.

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START
Web

START Sequence Tag Analysis and Reporting Tool

Allows comprehensive analysis of serial analysis of chromatin occupancy…

Allows comprehensive analysis of serial analysis of chromatin occupancy technique (SACO) data. START is applicable to experiments performed in the yeast, fruit fly, mouse, rat and human genomes. It…

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Skyline…
Web

Skyline nucleosome browser

Offers a suite of many algorithms and programs for the identification of…

Offers a suite of many algorithms and programs for the identification of nucleosome peaks over the genome. The Skyline nucleosome browser is a web-based application that permits users can access…

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