Package: ChIPXpress 1.57.2

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_1.57.2.tar.gz
ChIPXpress_1.57.2.zip(r-4.7-any)ChIPXpress_1.57.2.zip(r-4.6-any)ChIPXpress_1.57.2.zip(r-4.5-any)
ChIPXpress_1.57.2.tgz(r-4.6-any)ChIPXpress_1.57.2.tgz(r-4.5-any)
ChIPXpress_1.57.2.tar.gz(r-4.7-any)ChIPXpress_1.57.2.tar.gz(r-4.6-any)
ChIPXpress_1.57.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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-1.57.2(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

4.08 score 3 scripts 467 downloads 3 mentions 3 exports 97 dependencies

Last updated from:674af9f9a4. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	365
linux-devel	NOTE	572
source / vignettes	OK	417
linux-release	NOTE	446
macos-release	NOTE	387
macos-oldrel	NOTE	460
windows-devel	NOTE	470
windows-release	NOTE	421
windows-oldrel	NOTE	440
wasm-release	OK	362

Exports:buildDatabase ChIPXpress cleanDatabase

Dependencies:abind affxparser affy affyio askpass BH biganalytics biglm bigmemory bigmemory.sri Biobase BiocFileCache BiocGenerics BiocManager Biostrings bit bit64 blob cachem ChIPXpressData cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray dplyr fastmap ff filelock 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 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::Sweave

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