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
Source text:
(Rhee and Pugh, 2011) Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell.
A ChIP-exo protocol for map transcription factor (TF) binding genome-wide. This…
A ChIP-exo protocol for map transcription factor (TF) binding genome-wide. This protocol uses an efficient DNA self-circularization step during library preparation. ChIP-nexus protocol combines the…
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…
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…
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…
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…
An algorithm to identify transcription factor binding sites from ChIP-seq and…
An algorithm to identify transcription factor binding sites from ChIP-seq and ChIP-exo data.
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…
Resolves the location of protein-DNA interactions and discovers explanatory DNA…
Resolves the location of protein-DNA interactions and discovers explanatory DNA sequence motifs. GEM integrates model of ChIP-Seq or ChIP-exo reads and proximal DNA sequences. It makes binding…
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