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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ChIPXpress")
In most cases, you don't need to download the package archive at all.
ChIPXpress
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
Bioconductor version: 2.14
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 <gewu at jhsph.edu>
Citation (from within R,
enter citation("ChIPXpress")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ChIPXpress")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPXpress")
| R Script | ChIPXpress | |
| Reference Manual |
Details
| biocViews | ChIPSeq, ChIPchip, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | GPL(>=2) |
| Depends | R (>= 2.10), ChIPXpressData |
| Imports | Biobase, GEOquery, frma, affy, bigmemory, biganalytics |
| Suggests | mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ChIPXpress_1.6.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.6 (Snow Leopard) | ChIPXpress_1.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | ChIPXpress_1.6.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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