ChIPXpress: ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
Version 1.18.0

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.

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AuthorGeorge Wu
Bioconductor views ChIPSeq ChIPchip
Date of publicationNone
MaintainerGeorge Wu <gewu@jhsph.edu>
LicenseGPL(>=2)
Version1.18.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPXpress")

Man pages

buildDatabase: Builds a new database of gene expression profiles from a...
ChIPXpress: ChIPXpress Ranking
ChIPXpress-package: ChIPXpress ranks TF target genes given predicted TF targets...
cleanDatabase: Cleans the annotated output from buildDatabase to the...
Oct4ESC_ChIPgenes: Predicted Oct4 bound genes in embryonic stem cells (ESC)...

Functions

ChIPXpress Man page Source code
ChIPXpress-package Man page
Oct4ESC_ChIPgenes Man page
buildDatabase Man page Source code
cleanDatabase Man page Source code

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/ChIPXpress.R
R/buildDatabase.R
R/cleanDatabase.R
build
build/vignette.rds
data
data/Oct4ESC_ChIPgenes.rda
inst
inst/doc
inst/doc/ChIPXpress.R
inst/doc/ChIPXpress.Rnw
inst/doc/ChIPXpress.pdf
inst/unitTests
inst/unitTests/test_all.R
man
man/ChIPXpress-package.Rd
man/ChIPXpress.Rd
man/Oct4ESC_ChIPgenes.Rd
man/buildDatabase.Rd
man/cleanDatabase.Rd
tests
tests/runTests.R
vignettes
vignettes/ChIPXpress.Rnw
ChIPXpress documentation built on May 20, 2017, 10 p.m.