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ChIP-exo software tools

High-throughput sequencing 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 and Pugh, 2011).

CexoR

OMIC_00519

CexoR

Strand specific peak-pair calling in ChIP-exo replicates.

Strand specific peak-pair calling in ChIP-exo replicates.

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…

Model based Analysis of ChIP-exo

OMIC_00520

Model based Analysis of ChIP-exo
MACE

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 resolution border detection. 4) Border matching.