This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

ChIPXpress

This is the development version of ChIPXpress; for the stable 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: Development (3.18)

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 <georgetwu at gmail.com>

Citation (from within R, enter citation("ChIPXpress")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ChIPXpress")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChIPXpress")
ChIPXpress PDF R Script
Reference Manual PDF

Details

biocViews ChIPSeq, ChIPchip, Software
Version 1.45.0
In Bioconductor since BioC 2.11 (R-2.15) (11 years)
License GPL(>=2)
Depends R (>= 2.10), ChIPXpressData
Imports Biobase, GEOquery, frma, affy, bigmemory, biganalytics
Linking To
Suggests mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ChIPXpress_1.45.0.tar.gz
Windows Binary
macOS Binary (x86_64) ChIPXpress_1.45.0.tgz
macOS Binary (arm64) ChIPXpress_1.45.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ChIPXpress
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ChIPXpress
Bioc Package Browser https://code.bioconductor.org/browse/ChIPXpress/
Package Short Url https://bioconductor.org/packages/ChIPXpress/
Package Downloads Report Download Stats