DNase-seq data analysis bioinformatics software tools

Sequencing of DNase I hypersensitive sites (DNase-seq) is a powerful technique for identifying cis-regulatory elements across the genome. Many people currently analyzing DNase-seq data are using tools designed for ChIP-seq work, but may be inappropriate for DNase-seq data.

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HOMER
Desktop

HOMER Hypergeometric Optimization of Motif EnRichment

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER…

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of…

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pyDNase
Desktop
Web

pyDNase

A library for analyzing DNase-seq data. Many people currently analyzing…

A library for analyzing DNase-seq data. Many people currently analyzing DNase-seq data are using tools designed for ChIP-seq work, but may be inappropriate for DNase-seq data where one is less…

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DNaseR
Desktop

DNaseR

Enables the identification of protein binding footprints in DNase I…

Enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data. The cumulative Skellam distribution function (package 'skellam') is…

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SSA
Web
Desktop

SSA Submodular Selection of Assays

Chooses a diverse panel of genomic assays that leverages methods from…

Chooses a diverse panel of genomic assays that leverages methods from submodular optimization. SSA serves as a model for how submodular optimization can be applied to other discrete problems in…

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ChiLin
Desktop

ChiLin

Automates quality controls and data analyses on ChIP-seq and DNase-seq data.…

Automates quality controls and data analyses on ChIP-seq and DNase-seq data. ChiLin generates comprehensive quality control reports that include comparisons with historical data derived from over…

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SeqPlots
Desktop

SeqPlots

Visualizes next-generation sequencing (NGS) signals and sequence motif…

Visualizes next-generation sequencing (NGS) signals and sequence motif densities along genomic features using average plots and heatmaps. It can also calculate sequence motif density profiles from…

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ALTRE
Web
Desktop

ALTRE ALTered Regulatory Elements

An R package and associated R Shiny web app for differential analysis of…

An R package and associated R Shiny web app for differential analysis of regulatory elements genome-wide using chromatin accessibility data, such as DNase-seq or ATAC-seq. Users can run the workflow…

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MuSERA
Desktop

MuSERA Multiple Sample Enriched Region Assessment

A broadly useful standalone tool for both interactive and batch analysis of…

A broadly useful standalone tool for both interactive and batch analysis of combined evidence from enriched regions (ERs) in multiple ChIP-seq or DNase-seq replicates. Besides rigorously combining…

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PeaKDEck
Desktop

PeaKDEck

A peak-calling algorithm written in Perl, mainly intended for use in the…

A peak-calling algorithm written in Perl, mainly intended for use in the identification of peaks in mapped DNaseI-seq data. PeaKDEck also includes a set of utilities for processing and manipulation…

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TEPIC
Desktop

TEPIC

Predicts transcription factors binding sites and epigenetic data by combining…

Predicts transcription factors binding sites and epigenetic data by combining sets of open-chromatin regions with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g.…

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DeFCoM
Desktop

DeFCoM Detecting Footprints Containing Motifs

A supervised learning based footprint prediction framework. DeFCoM was designed…

A supervised learning based footprint prediction framework. DeFCoM was designed to capture variation in DNaseI signal within active footprints and unbound motif sites to enhance footprint…

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Mocap
Desktop

Mocap

Integrates chromatin accessibility, motif scores, TF footprints, CpG/GC…

Integrates chromatin accessibility, motif scores, TF footprints, CpG/GC content, evolutionary conservation and other factors in an ensemble of TFCT-specific classifiers. Mocap uses sequence-derived…

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Romulus
Desktop

Romulus

A computational method for identifying individual transcription factor (TF)…

A computational method for identifying individual transcription factor (TF) binding sites from genome sequence information and cell-type–specific experimental data, such as DNase-seq. Romulus…

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CENTIPEDE
Desktop

CENTIPEDE

Applies a hierarchical Bayesian mixture model to infer regions of the genome…

Applies a hierarchical Bayesian mixture model to infer regions of the genome that are bound by particular transcription factors (TFs). CENTIPEDE starts by identifying a set of candidate binding sites…

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FootprintMixtur…
Desktop

FootprintMixture

A mixture modeling framework to train multinomial based footprint models and…

A mixture modeling framework to train multinomial based footprint models and assign footprint likelihood scores to each candidate binding site. The modeling approach was also able to detect variation…

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DNase2TF
Desktop

DNase2TF

An efficient footprint detection program. DNase2TF searches for relatively…

An efficient footprint detection program. DNase2TF searches for relatively protected regions within DNase I hypersensitive sites and generates a set of footprint candidates at a preset FDR threshold.…

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HINT
Desktop

HINT Hmm-based IdeNtification of Tf footprints

A method based on hidden Markov models to integrate DNase I hypersensitivity…

A method based on hidden Markov models to integrate DNase I hypersensitivity and histone modifications occupancy for the detection of open chromatin regions and active binding sites. We have created…

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PIQ
Desktop

PIQ Protein Interaction Quantitation

A computational method for modeling the magnitude and shape of genome-wide…

A computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning…

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msCentipede
Desktop

msCentipede

An algorithm for accurately inferring transcription factor binding sites using…

An algorithm for accurately inferring transcription factor binding sites using chromatin accessibility data (DNase-seq, ATAC-seq). The hierarchical multiscale model underlying msCentipede identifies…

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DFilter
Desktop

DFilter

A detection algorithm that identifies regulatory features in ChIP-seq,…

A detection algorithm that identifies regulatory features in ChIP-seq, DNase-seq and FAIRE-seq data more accurately than assay-specific algorithms. The mathematical formalism underlying DFilter…

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BinDNase
Desktop

BinDNase

A discriminative algorithm for predicting TF-DNA interaction sites using…

A discriminative algorithm for predicting TF-DNA interaction sites using DNase-seq data. BinDNase implements an efficient method for selecting and extracting informative features from DNase I signal…

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cERMIT
Desktop

cERMIT

Pipeline for analysis of deep sequencing data (ChIP-seq, DNaseI-seq).

Pipeline for analysis of deep sequencing data (ChIP-seq, DNaseI-seq).

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LR-DNase
Algorithm

LR-DNase logistic regression DNase

A logistic regression model. LR-DNase predicts binding sites for a specific…

A logistic regression model. LR-DNase predicts binding sites for a specific transcription factor (TF) using seven features derived from DNase-seq and genomic sequence. We calculate the area under the…

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