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chipseqDB

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


Bioconductor version: Release (3.18)

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 "4.3") 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")
1. Introduction HTML
2. Differential enrichment of H3K9ac in B cells HTML
3. Differential binding of CBP in fibroblasts HTML R Script
4. Differential enrichment of H3K27me3 in lung epithelium HTML

Details

biocViews EpigeneticsWorkflow, ImmunoOncologyWorkflow, Workflow
Version 1.26.0
License Artistic-2.0
Depends
Imports
System Requirements
URL https://www.bioconductor.org/help/workflows/chipseqDB/
See More
Suggests chipseqDBData, BiocStyle, BiocFileCache, ChIPpeakAnno, Gviz, Rsamtools, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR, knitr, org.Mm.eg.db, rtracklayer, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
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Package Archives

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

Source Package chipseqDB_1.26.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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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