ChIPXpress
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
Bioconductor version: 3.23 · Package version: 1.56.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChIPXpress")Details
| Maintainer | George Wu <georgetwu@gmail.com> |
| Author | George Wu |
| License | GPL(>=2) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ChIPSeq, ChIPchip, Software |
| Package Short Url | https://bioconductor.org/packages/ChIPXpress/ |
Citation
From within R, enter citation("ChIPXpress"):
George Wu. ChIPXpress: ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles. doi:10.18129/B9.bioc.ChIPXpress, R package version 1.56.0, https://bioconductor.org/packages/ChIPXpress.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ChIPXpress_1.56.0.tar.gz |
| Windows binary (x86_64) | ChIPXpress_1.56.0.zip |
| macOS binary (arm64) | ChIPXpress_1.56.0.tgz |
| macOS binary (x86_64) | ChIPXpress_1.56.0.tgz |
Dependencies
Depends: R (>= 2.10), ChIPXpressData
Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics
Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics