ChIPXpress

DOI: 10.18129/B9.bioc.ChIPXpress    

This package is for version 3.15 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: 3.15

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 "4.2") and enter:

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

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")

 

PDF	R Script	ChIPXpress
PDF		Reference Manual

Details

biocViews	ChIPSeq, ChIPchip, Software
Version	1.40.0
In Bioconductor since	BioC 2.11 (R-2.15) (10 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
Links To Me
Build Report

Package Archives

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

Source Package	ChIPXpress_1.40.0.tar.gz
Windows Binary
macOS Binary (x86_64)	ChIPXpress_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ChIPXpress
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChIPXpress
Package Short Url	https://bioconductor.org/packages/ChIPXpress/
Package Downloads Report	Download Stats