Workflow Package: chipseqDB

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data

Bioconductor version: Release (3.8)

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 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 <infinite.monkeys.with.keyboards at gmail.com>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("chipseqDB", version = "3.8")

Documentation

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

browseVignettes("chipseqDB")

 

HTML R Script 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

Details

biocViews EpigeneticsWorkflow, Workflow
Version 1.4.0
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
LinkingTo
Suggests knitr, rmarkdown
SystemRequirements
Enhances
URL https://www.bioconductor.org/help/workflows/chipseqDB/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

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