chipseqDB

This is the released version of chipseqDB; for the devel version, see chipseqDB.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

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

Bioconductor version: Release (3.23)

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")):

Aaron Lun, Gordon Smyth. chipseqDB: A Bioconductor Workflow to Detect Differential Binding in ChIP-seq Data. doi:10.18129/B9.bioc.chipseqDB, R package version 1.36.0, https://bioconductor.org/packages/chipseqDB.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	EpigeneticsWorkflow, ImmunoOncologyWorkflow, Workflow
Version	1.36.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
License	Artistic-2.0
Depends
Imports
System Requirements
URL	https://www.bioconductor.org/help/workflows/chipseqDB/

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
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	chipseqDB_1.36.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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/
Package Downloads Report	Download Stats