ChIPXpress
This package is for version 3.9 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: 3.9
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("ChIPXpress")):
Installation
To install this package, start R (version "3.6") 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")| ChIPXpress | R Script | |
| Reference Manual |
Details
| biocViews | ChIPSeq, ChIPchip, Software |
| Version | 1.28.0 |
| 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 | |
| URL |
See More
| Suggests | mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChIPXpress_1.28.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | ChIPXpress_1.28.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |