An R/Bioconductor package for gene set analysis
Overview of piano
Gene set analysis using a variety of methods
Piano is used for running gene set analysis (GSA) using a selection of available methods (some of which are also implemented in separate packages or other software) and starting from different kinds of gene level statistics. The advantage with using piano is that all of these methods can be run using the same setup, resulting in minimal effort for the user when switching between methods.
Directionality of gene sets
Piano contains a new approach which divides the gene set results into directionality classes, giving deeper information about the underlying gene pattern. For details, see the publication below.
Consensus gene set analysis
Piano contains functions to perform consensus analysis, i.e. combining the results of multiple GSA runs.
Explore GSA results in an interactive Shiny app
Using the function
exploreGSAres one can interactively and visually explore the GSA results. See a demo here (note that the app will run substantially smoother when launching it locally from within R).
Please cite the piano publication if you use it in your research:
Väremo, L., Nielsen, J. and Nookaew, I. (2013) Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Research. 41 (8), 4378-4391. https://doi.org/10.1093/nar/gkt111
Email the developer at piano.rpkg (at) gmail.com. If you encountered any problems please check if your questions are already answered on the help page, in the vignette or in the function documentation before you email for support.
You may also file an issue or pull request directly on GitHub.
This work was carried out at Systems and Synthetic Biology at Chalmers University of Technology, Gothenburg, Sweden. Funding was provided from Knut and Alice Wallenberg foundation, Chalmers foundation and Bioinformatics Infrastructure for Life Sciences (BILS). The computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at C3SE.
Current development and maintenance is carried out in affiliation with the National Bioinformatics Infrastructure Sweden (NBIS).