chipseqDB
A Bioconductor Workflow to Detect Differential Binding in ChIP-seq Data
Bioconductor version: Release (3.17)
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("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 | 1.24.0 |
| License | Artistic-2.0 |
| Depends | |
| Imports | |
| Linking To | |
| Suggests | chipseqDBData, BiocStyle, BiocFileCache, ChIPpeakAnno, Gviz, Rsamtools, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR, knitr, org.Mm.eg.db, rtracklayer, rmarkdown |
| System Requirements | |
| Enhances | |
| URL | https://www.bioconductor.org/help/workflows/chipseqDB/ |
See More
| 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_1.24.0.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/ |
| Package Downloads Report | Download Stats |