This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see chipseqDB.

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data

Bioconductor version: 3.8

Describes a computational workflow for performing a DB analysis with sliding windows. The aim is to facilitate the practical implementation of window-based DB analyses by providing detailed code and expected output. The workflow described here applies to any ChIP-seq experiment with multiple experimental conditions and multiple biological samples in one or more of the conditions. It detects and summarizes DB regions between conditions in a *de novo* manner, i.e., without making any prior assumptions about the location or width of bound regions. Detected regions are then annotated according to their proximity to annotated genes. In addition, the code can be easily adapted to accommodate batch effects, covariates and multiple experimental factors.

Author: Aaron Lun [aut, cre], Gordon Smyth [aut]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at>

Citation (from within R, enter citation("chipseqDB")):


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HTML R Script Detecting differential binding of CBP in mouse fibroblasts
HTML R Script Detecting differential enrichment of H3K9ac in murine B cells
HTML R Script From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data


biocViews EpigeneticsWorkflow, ImmunoOncologyWorkflow, Workflow
Version 1.4.1
License Artistic-2.0
Depends R (>= 3.3.0), BiocStyle, ChIPpeakAnno, Gviz, Rsamtools, Rsubread, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR, knitr, locfit,, rtracklayer, statmod
Suggests knitr, rmarkdown
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Source Package chipseqDB_1.4.1.tar.gz
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