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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ChIPseqR")
In most cases, you don't need to download the package archive at all.
ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing Data
Bioconductor version: 2.14
ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.
Author: Peter Humburg
Maintainer: Peter Humburg <peter.humburg at well.ox.ac.uk>
Citation (from within R,
enter citation("ChIPseqR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ChIPseqR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPseqR")
| R Script | Introduction to ChIPseqR | |
| Reference Manual |
Details
| biocViews | ChIPSeq, Infrastructure, Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10.0), methods, BiocGenerics, ShortRead |
| Imports | Biostrings, fBasics, GenomicRanges, graphics, grDevices, HilbertVis, IRanges, methods, ShortRead, stats, timsac, utils |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ChIPseqR_1.18.0.tar.gz |
| Windows Binary | ChIPseqR_1.18.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ChIPseqR_1.18.0.tgz |
| Mac OS X 10.9 (Mavericks) | ChIPseqR_1.18.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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