piano-package: Piano - Platform for Integrative ANalysis of Omics data
In piano: Platform for integrative analysis of omics data

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Run gene set analysis with various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.

The Piano package consists of two parts. The major part revolves around gene set analysis (GSA), and the central function for this is runGSA. There are some downstream functions (e.g. GSAsummaryTable and geneSetSummary) that handle the results from the GSA. By running runGSA multiple times with different settings it is possible to compute consensus gene set scores. Another set of functions (e.g. consensusScores and consensusHeatmap) take a list of result objects given by runGSA for this step. The second part of the Piano package contains a set of functions devoted for an easy-to-use approach on microarray analysis (wrapped around the affy and limma packages), which are constructed to integrate nicely with the downstream GSA part. The starting function in this case is loadMAdata.