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…
Desktop app
G T A T C G C T A CexoR CexoR

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…

Desktop app
G T A T C G C T A Model based Analysis… Model based Analysis of ChIP-exo

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…

Desktop app
G T A T C G C T A ChIP experiments with… ChIP experiments with Nucleotide resolution…
Desktop app
G T A T C G C T A PeakXus PeakXus

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…

G T A T C G C T A Protein Attached… Protein Attached Chromatin Capure

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…

Desktop app
G T A T C G C T A Q-nexus Q-nexus

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…

Desktop app
G T A T C G C T A DFilter DFilter

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…

Related Websites
Advertisements
Join Omic Community

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.