chipseqDB

DOI: 10.18129/B9.bioc.chipseqDB    

This is the development version of chipseqDB; to use it, please install the devel version of Bioconductor.

A Bioconductor Workflow to Detect Differential Binding in ChIP-seq Data

Bioconductor version: Development (3.10)

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 genes.

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

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

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

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

HTML R Script 1. Introduction
HTML R Script 2. Differential enrichment of H3K9ac in B cells
HTML R Script 3. Differential binding of CBP in fibroblasts
HTML R Script 4. Differential enrichment of H3K27me3 in lung epithelium

Details

biocViews EpigeneticsWorkflow, ImmunoOncologyWorkflow, Workflow
Version 1.9.4
License Artistic-2.0
Depends
Imports
LinkingTo
Suggests chipseqDBData, BiocStyle, BiocFileCache, ChIPpeakAnno, Gviz, Rsamtools, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR, knitr, org.Mm.eg.db, rtracklayer, rmarkdown
SystemRequirements
Enhances
URL https://www.bioconductor.org/help/workflows/chipseqDB/
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

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

Source Package chipseqDB_1.9.4.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/
Package Downloads Report Download Stats

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