To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("iChip")
In most cases, you don't need to download the package archive at all.
iChip
Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
Bioconductor version: 3.0
This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. It can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.
Author: Qianxing Mo
Maintainer: Qianxing Mo <qmo at bcm.edu>
Citation (from within R,
enter citation("iChip")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("iChip")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("iChip")
| R Script | iChip | |
| Reference Manual |
Details
| biocViews | AgilentChip, ChIPchip, Microarray, OneChannel, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10.0) |
| Imports | limma |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | iChip_1.20.0.tar.gz |
| Windows Binary | iChip_1.20.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | iChip_1.20.0.tgz |
| Mac OS X 10.9 (Mavericks) | iChip_1.20.0.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
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
