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

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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.

Author
George Wu
Date of publication
None
Maintainer
George Wu <gewu@jhsph.edu>
License
GPL(>=2)
Version
1.16.0

View on Bioconductor

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)...

Files in this package

ChIPXpress/.BBSoptions
ChIPXpress/DESCRIPTION
ChIPXpress/NAMESPACE
ChIPXpress/R
ChIPXpress/R/ChIPXpress.R
ChIPXpress/R/buildDatabase.R
ChIPXpress/R/cleanDatabase.R
ChIPXpress/build
ChIPXpress/build/vignette.rds
ChIPXpress/data
ChIPXpress/data/Oct4ESC_ChIPgenes.rda
ChIPXpress/inst
ChIPXpress/inst/doc
ChIPXpress/inst/doc/ChIPXpress.R
ChIPXpress/inst/doc/ChIPXpress.Rnw
ChIPXpress/inst/doc/ChIPXpress.pdf
ChIPXpress/inst/unitTests
ChIPXpress/inst/unitTests/test_all.R
ChIPXpress/man
ChIPXpress/man/ChIPXpress-package.Rd
ChIPXpress/man/ChIPXpress.Rd
ChIPXpress/man/Oct4ESC_ChIPgenes.Rd
ChIPXpress/man/buildDatabase.Rd
ChIPXpress/man/cleanDatabase.Rd
ChIPXpress/tests
ChIPXpress/tests/runTests.R
ChIPXpress/vignettes
ChIPXpress/vignettes/ChIPXpress.Rnw