ChIPXpress

DOI: 10.18129/B9.bioc.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>

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

PDF		Reference Manual

Details

biocViews	ChIPSeq, ChIPchip, Software
Version	1.45.0
In Bioconductor since	BioC 2.11 (R-2.15) (10.5 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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)	ChIPXpress_1.45.0.tgz
macOS Binary (arm64)
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