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Computational Analysis of ChIP-seq Data
2010Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a new technology to map protein-DNA interactions in a genome. The genome-wide transcription factor binding site and chromatin modification data produced by ChIP-seq provide invaluable information for studying gene regulation. This chapter reviews basic characteristics
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Modelling ChIP-seq Data Using HMMs
2017Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) experiments have now become routine in biology for the detection of protein binding sites. In this chapter, we show how hidden Markov models can be used for the analysis of data generated by ChIP-seq experiments.
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Statistical Analysis of ChIP-seq Data with MOSAiCS
2013Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is invaluable for identifying genome-wide binding of transcription factors and mapping of epigenomic profiles. We present a statistical protocol for analyzing ChIP-seq data.
Guannan, Sun +3 more
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2015
Introduction to ChIP-seq data analysis. Overview of quality control, mapping, peak calling and downstream analysis methods.
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Introduction to ChIP-seq data analysis. Overview of quality control, mapping, peak calling and downstream analysis methods.
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Methods for ChIP-seq analysis: A practical workflow and advanced applications
Methods, 2021Ryuichiro Nakato, Toyonori Sakata
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ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates
Genomics, 2021Rhys Newell +2 more
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CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis
Genomics, Proteomics and Bioinformatics, 2021Henry W Long +2 more
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ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data
EMBO Reports, 2018Osamu Ogasawara +2 more
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ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions
Methods, 2009Duncan Odom +2 more
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