Package: ChIPXpress 1.56.0

George Wu

ChIPXpress: ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles

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.

Authors:George Wu

ChIPXpress_1.56.0.tar.gz
ChIPXpress_1.56.0.zip(r-4.7)ChIPXpress_1.56.0.zip(r-4.6)ChIPXpress_1.56.0.zip(r-4.5)
ChIPXpress_1.56.0.tgz(r-4.6-any)ChIPXpress_1.56.0.tgz(r-4.5-any)
ChIPXpress_1.56.0.tar.gz(r-4.7-any)ChIPXpress_1.56.0.tar.gz(r-4.6-any)
ChIPXpress_1.56.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ChIPXpress/json (API)

# Install 'ChIPXpress' in R:

install.packages('ChIPXpress', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

Oct4ESC_ChIPgenes - Predicted Oct4 bound genes in embryonic stem cells (ESC) obtained from analyzing ChIP-seq data

On BioConductor:ChIPXpress-1.57.0(bioc 3.24)ChIPXpress-1.56.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

chipchip chipseq

3.78 score 6 scripts 398 downloads 3 mentions 3 exports 95 dependencies

Last updated from:ca57a31185 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	428
linux-devel-x86_64	NOTE	575
source / vignettes	OK	496
linux-release-x86_64	NOTE	574
macos-release-arm64	NOTE	470
macos-oldrel-arm64	NOTE	316
windows-devel	NOTE	441
windows-release	NOTE	469
windows-oldrel	NOTE	543
wasm-release	OK	367

Exports:buildDatabase ChIPXpress cleanDatabase

Dependencies:abind affxparser affy affyio askpass BH biganalytics biglm bigmemory bigmemory.sri Biobase BiocGenerics BiocManager Biostrings bit bit64 blob cachem ChIPXpressData cli clipr codetools cpp11 crayon curl data.table DBI DelayedArray dplyr fastmap ff foreach frma generics GenomicRanges GEOquery glue hms httr httr2 IRanges iterators jsonlite lattice lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mime oligo oligoClasses openssl pillar pkgconfig preprocessCore prettyunits progress purrr R.methodsS3 R.oo R.utils R6 rappdirs Rcpp readr rentrez rlang RSQLite rvest S4Arrays S4Vectors selectr Seqinfo SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb utf8 uuid vctrs vroom withr XML xml2 XVector

ChIPXpress

Rendered fromChIPXpress.Rnwusingutils::Sweaveon May 29 2026.

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ChIPXpress ranks TF target genes given predicted TF targets from ChIP-chip and ChIP-seq data using publicly available gene expression data	ChIPXpress-package
Builds a new database of gene expression profiles from a specified platform or sample files in NCBI GEO.	buildDatabase
ChIPXpress Ranking	ChIPXpress
Cleans the annotated output from buildDatabase to the required format for ChIPXpress analyses	cleanDatabase
Predicted Oct4 bound genes in embryonic stem cells (ESC) obtained from analyzing ChIP-seq data	Oct4ESC_ChIPgenes