chipseqDB
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see chipseqDB.
From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data
Bioconductor version: 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("chipseqDB")):
Installation
To install this package, start R (version "3.5") 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")| 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 | HTML | R Script |
Details
| biocViews | EpigeneticsWorkflow, ImmunoOncologyWorkflow, Workflow |
| Version | 1.4.1 |
| 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 | |
| System Requirements | |
| URL | https://www.bioconductor.org/help/workflows/chipseqDB/ |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| 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_1.4.1.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 [email protected]:packages/chipseqDB |
| Package Short Url | https://bioconductor.org/packages/chipseqDB/ |
| Package Downloads Report | Download Stats |