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ChIPXpress (version 1.14.0)

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

Description

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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Version

Version

1.14.0

License

GPL(>=2)

Maintainer

George Wu

Last Published

February 15th, 2017

Functions in ChIPXpress (1.14.0)

cleanDatabase

Cleans the annotated output from buildDatabase to the required format for ChIPXpress analyses
ChIPXpress

ChIPXpress Ranking
ChIPXpress-package

ChIPXpress ranks TF target genes given predicted TF targets from ChIP-chip and ChIP-seq data using publicly available gene expression data
buildDatabase

Builds a new database of gene expression profiles from a specified platform or sample files in NCBI GEO.
Oct4ESC_ChIPgenes

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