chipseqDB

This package is for version 3.7 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: 3.7

This article 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 with multiple biological samples within 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 <alun at wehi.edu.au>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("chipseqDB")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("chipseqDB")
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 HTML R Script

Details

biocViews EpigeneticsWorkflow, Workflow
Version 1.2.0
License Artistic-2.0
Depends R (>= 3.3.0), BiocStyle, ChIPpeakAnno, Gviz, Rsamtools, Rsubread, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR, knitr, locfit, org.Mm.eg.db, rtracklayer, statmod
Imports
System Requirements
URL https://www.bioconductor.org/help/workflows/chipseqDB/
See More
Suggests knitr, rmarkdown
Linking To
Enhances
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package chipseqDB_1.2.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository git clone https://git.bioconductor.org/packages/chipseqDB
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chipseqDB
Package Short Url https://bioconductor.org/packages/chipseqDB/
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