ChIP-exonuclease data analysis bioinformatics software tools
ChIP-exo allows to determine genomic locations of a known protein associated with genomic DNA sequences at near nucleotide resolution using a combination of chromatin immunoprecipitation (ChIP) and lambda exonuclease digestion (exo) followed by high-throughput sequencing (Rhee…
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CexoR
Desktop

CexoR

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative…

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalised count differences of…

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MACE
Desktop

MACE Model based Analysis of ChIP-exo

A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth…

A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth normalization and nucleotide composition bias correction. 2) Signal consolidation and noise reduction. 3) Single base…

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ChIP-nexus
Desktop
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PeakXus
Desktop

PeakXus

A peak caller specifically designed to leverage the increased accuracy of novel…

A peak caller specifically designed to leverage the increased accuracy of novel experimental methods for studying transcription factor (TF) binding in vivo in an unbiased manner. Our emphasis is on…

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PAtCh-Cap
Algorithm

PAtCh-Cap Protein Attached Chromatin Capure

A method for non-specifically capturing cross-linked chromatin complexes via…

A method for non-specifically capturing cross-linked chromatin complexes via protein carboxylate groups that allows the DNA to be subjected to all downstream chemical treatments. PAtCh-Cap is…

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Q-nexus
Desktop

Q-nexus

A method for the estimation of the protected-region width and peak calling that…

A method for the estimation of the protected-region width and peak calling that can be applied to ChIP-nexus as well as ChIP-exo data. Q-nexus creates pseudo-controls from the data with which true…

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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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