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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPXpress")
In most cases, you don't need to download the package archive at all.
ChIPXpress
|
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see ChIPXpress.
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
Bioconductor version: 3.0
ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.
Author: George Wu
Maintainer: George Wu <gewu at jhsph.edu>
Citation (from within R,
enter citation("ChIPXpress")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPXpress")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPXpress")
| R Script | ChIPXpress | |
| Reference Manual |
Details
| biocViews | ChIPSeq, ChIPchip, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (3.5 years) |
| License | GPL(>=2) |
| Depends | R (>= 2.10), ChIPXpressData |
| Imports | Biobase, GEOquery, frma, affy, bigmemory, biganalytics |
| LinkingTo | |
| Suggests | mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics |
| 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 | ChIPXpress_1.8.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.6 (Snow Leopard) | ChIPXpress_1.8.0.tgz |
| Mac OS X 10.9 (Mavericks) | ChIPXpress_1.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/ChIPXpress/tree/release-3.0 |
| Package Short Url | http://bioconductor.org/packages/ChIPXpress/ |
| Package Downloads Report | Download Stats |
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