chipseqDB

DOI: 10.18129/B9.bioc.chipseqDB    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see chipseqDB.

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

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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	1.14.0
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_1.14.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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