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 2.11 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: 2.11

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")
PDF R Script ChIPXpress
PDF Reference Manual

Details

biocViews Bioinformatics, ChIPchip, ChIPseq, Software
Version 1.0.0
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_1.0.0.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ChIPXpress/tree/release-2.11
Package Short Url http://bioconductor.org/packages/ChIPXpress/
Package Downloads Report Download Stats

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