Package: ChIPXpress 1.51.0

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_1.51.0.tar.gz
ChIPXpress_1.51.0.zip(r-4.5)ChIPXpress_1.51.0.zip(r-4.4)ChIPXpress_1.51.0.zip(r-4.3)
ChIPXpress_1.51.0.tgz(r-4.4-any)ChIPXpress_1.49.0.tgz(r-4.3-any)
ChIPXpress_1.51.0.tar.gz(r-4.5-noble)ChIPXpress_1.51.0.tar.gz(r-4.4-noble)
ChIPXpress_1.51.0.tgz(r-4.4-emscripten)ChIPXpress_1.51.0.tgz(r-4.3-emscripten)
ChIPXpress.pdf |ChIPXpress.html✨
ChIPXpress/json (API)

# Install 'ChIPXpress' in R:

install.packages('ChIPXpress', repos = c('https://bioc.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-1.49.0(bioc 3.20)ChIPXpress-1.48.0(bioc 3.19)

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

chipchip chipseq

3.30 score 2 scripts 218 downloads 3 exports 100 dependencies

Last updated 26 days agofrom:498fd5fbb7. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 30 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 30 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Oct 30 2024
R-4.3-mac	NOTE	Oct 06 2024

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 fansi fastmap ff foreach frma generics GenomeInfoDb GenomeInfoDbData GenomicRanges GEOquery glue hms httr httr2 IRanges iterators jsonlite lattice lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mime oligo oligoClasses openssl pillar pkgconfig plogr preprocessCore prettyunits progress purrr R.methodsS3 R.oo R.utils R6 rappdirs Rcpp readr rentrez rlang RSQLite rvest S4Arrays S4Vectors selectr SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb UCSC.utils utf8 uuid vctrs vroom withr XML xml2 XVector zlibbioc

ChIPXpress

Rendered fromChIPXpress.Rnwusingutils::Sweaveon Oct 30 2024.

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