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RnaChipIntegrator is a utility that performs integrated analyses of RNA-Seq and ChIP-Seq data, identifying the nearest ChIP peaks to each transcript, and vice versa. The individual analyses differ from each other according to the criteria that are used to calculate the distances between peaks and transcripts.

The program was originally written specifically for ChIP-Seq and RNA-Seq data but can be used with any set of genomic features e.g. canonical genes, CpG islands etc, or expression data e.g. microarrays.

See the project's homepage at http://fls-bioinformatics-core.github.com/RnaChipIntegrator/ for download, installation and usage information.