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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 (3.19)

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 "4.4") 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 1.47.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License GPL(>=2)
Depends R (>= 2.10), ChIPXpressData
Imports Biobase, GEOquery, frma, affy, bigmemory, biganalytics
System Requirements
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Suggests mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics
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Package Archives

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

Source Package ChIPXpress_1.47.0.tar.gz
Windows Binary
macOS Binary (x86_64) ChIPXpress_1.47.0.tgz
macOS Binary (arm64) ChIPXpress_1.47.0.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/
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