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DNase-seq software tools

High-throughput sequencing 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.

BinDNase

OMIC_08436

BinDNase

A discriminative algorithm for predicting TF-DNA interaction sites using DNase-seq data.…

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 for each TF, either at single nucleotide…

CENTIPEDE

OMIC_11375

CENTIPEDE

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

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 (e.g., sites that match a certain position weight…

cERMIT

OMIC_05268

cERMIT

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

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

DFilter

OMIC_08442

DFilter

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

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 facilitates integrative analysis of data from virtually…

DNase2TF

OMIC_11373

DNase2TF

An efficient footprint detection program. DNase2TF searches for relatively protected…

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. Starting with an empirical set of candidate…

DNaseR

OMIC_00517

DNaseR

Enables the identification of protein binding footprints in DNase I hypersensitive sites…

Enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data. The cumulative Skellam distribution function (package ‘skellam’) is used to detect significant normalized count…

FootprintMixture

OMIC_11374

FootprintMixture

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

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 in the consensus motifs that transcription…

Hmm-based IdeNtification of Tf footprints

OMIC_11372

Hmm-based IdeNtification of Tf footprints
HINT

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

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 a framework that includes treatment of genomic…

msCentipede

OMIC_10694

msCentipede

An algorithm for accurately inferring transcription factor binding sites using chromatin…

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

PeaKDEck

OMIC_02207

PeaKDEck

A peak-calling programme for DNAseI-seq data.

A peak-calling programme for DNAseI-seq data.

Protein Interaction Quantitation

OMIC_11371