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
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
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
cERMIT
Pipeline for analysis of deep sequencing data (ChIP-seq, DNaseI-seq).
Pipeline for analysis of deep sequencing data (ChIP-seq, DNaseI-seq).
DFilter
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
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
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
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
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
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
PeaKDEck
A peak-calling programme for DNAseI-seq data.
A peak-calling programme for DNAseI-seq data.
Protein Interaction Quantitation
Protein Interaction Quantitation
PIQ
A computational method for modeling the magnitude and shape of genome-wide DNase I…
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 techniques, PIQ identified binding sites for…
pyDNase
pyDNase
A library for analyzing DNase-seq data. Many people currently analyzing DNase-seq data…
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 interested in the overlaps of sequenced fragments, but…