chipseqDB
This package is for version 3.10 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: 3.10
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 "3.6") 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")| 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 | HTML | R Script |
Details
| biocViews | EpigeneticsWorkflow, ImmunoOncologyWorkflow, Workflow |
| Version | 1.10.0 |
| 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 |
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| 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_1.10.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | |
| 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 |