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Nucleosome positioning software tools | MNase-seq analysis

Nucleosomes consisting of approximately 146 base pairs (bp) of DNA wrapped around a histone octamer are the fundamental structural units of chromatin in metazoans (Kornberg and Lorch, 1999; Kornberg and Lorch, 2002). The translational…
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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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nucleR
Desktop

nucleR

A package for non-parametric nucleosome positioning. nucleR uses a novel…

A package for non-parametric nucleosome positioning. nucleR uses a novel aproach in this field which comprises a deep profile cleaning using Fourier Transform and peak scoring for a quick and…

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NOrMAL
Desktop

NOrMAL

A command line tool for accurate placing of the nucleosomes. NOrMAL was…

A command line tool for accurate placing of the nucleosomes. NOrMAL was designed to resolve overlapping nucleosomes and extract extra information ("fuzziness", probability, etc.) of…

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Pasha
Desktop

Pasha Preprocessing of Aligned Sequences from HTS Analyses

An R package designed for processing aligned reads from chromatin-oriented…

An R package designed for processing aligned reads from chromatin-oriented high-throughput sequencing experiments. Pasha allows easy manipulation of aligned reads from short-read sequencing…

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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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NucleoFinder
Desktop

NucleoFinder

Addresses both the positional heterogeneity across cells and experimental…

Addresses both the positional heterogeneity across cells and experimental biases by seeking nucleosomes consistently positioned in a cell population and showing a significant enrichment relative to a…

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iNPS
Desktop

iNPS

NPS is a widely used software package for detecting nucleosome positions from…

NPS is a widely used software package for detecting nucleosome positions from MNase-seq data, but its accuracy needs much improvement. iNPS was improved by adding two major modifications to NPS to…

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