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