ChIPXpress

ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles

Bioconductor version: Development (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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("ChIPXpress")

To cite this package in a publication, start R and enter:

    citation("ChIPXpress")

Documentation

PDF R Script ChIPXpress
PDF   Reference Manual

Details

biocViews ChIPSeq, ChIPchip, Software
Version 1.7.0
In Bioconductor since BioC 2.11 (R-2.15)
License GPL(>=2)
Depends R (>= 2.10), ChIPXpressData
Imports Biobase, GEOquery, frma, affy, bigmemory, biganalytics
Suggests mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source ChIPXpress_1.7.0.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard) ChIPXpress_1.7.0.tgz
Mac OS X 10.9 (Mavericks)
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