piano: Platform for integrative analysis of omics data

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Piano performs gene set analysis using 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.

Author
Leif Varemo <piano.rpkg@gmail.com> and Intawat Nookaew <piano.rpkg@gmail.com>
Date of publication
None
Maintainer
Leif Varemo <piano.rpkg@gmail.com>
License
GPL (>=2)
Version
1.14.4
URLs

View on Bioconductor

Man pages

consensusHeatmap
Heatmap of top consensus gene sets
consensusScores
Top consensus gene sets and boxplot
diffExp
Perform differential expression analysis
extractFactors
Extracts 'ArrayData' factors
geneSetSummary
Gene set summary
GSAheatmap
Heatmap of top significant gene sets
gsa_input
Random input data for gene set analysis
gsa_results
Gene set analysis result data
GSAsummaryTable
Gene set analysis summary table
loadGSC
Load a gene set collection
loadMAdata
Load and preprocess microarray data
networkPlot
Gene set network plot
piano-package
Piano - Platform for Integrative ANalysis of Omics data
polarPlot
Polar plot
runGSA
Gene set analysis
runGSAhyper
Gene set analysis with Fisher's exact test
runQC
Run quality control
writeFilesForKiwi
Write files for Kiwi

Files in this package

piano/DESCRIPTION
piano/NAMESPACE
piano/NEWS
piano/R
piano/R/GSAheatmap.R
piano/R/GSAsummaryTable.R
piano/R/GSCsignificanceBatch.R
piano/R/GSCstatBatch.R
piano/R/GSCstatGenePerm.R
piano/R/GSCstatSamplePerm.R
piano/R/calcGeneSetStat.R
piano/R/checkLoadArg.r
piano/R/consensusHeatmap.R
piano/R/consensusScores.R
piano/R/diffExp.r
piano/R/extractFactors.r
piano/R/fdrGSEA.R
piano/R/geneSetSummary.R
piano/R/loadGSC.R
piano/R/loadMAdata.r
piano/R/networkPlot.R
piano/R/polarPlot.r
piano/R/print_ArrayData.r
piano/R/print_GSAres.R
piano/R/print_GSC.R
piano/R/pvalFromDistribution.R
piano/R/pvalFromFractionGenePerm.R
piano/R/pvalFromFractionSamplePerm.R
piano/R/runGSA.r
piano/R/runGSAhyper.R
piano/R/runQC.r
piano/R/writeFilesForKiwi.R
piano/build
piano/build/vignette.rds
piano/data
piano/data/gsa_input.RData
piano/data/gsa_results.RData
piano/inst
piano/inst/CITATION
piano/inst/doc
piano/inst/doc/piano-vignette.R
piano/inst/doc/piano-vignette.Rnw
piano/inst/doc/piano-vignette.pdf
piano/inst/extdata
piano/inst/extdata/norm_data.txt.gz
piano/inst/extdata/probe2metabolites_iIN800.txt.gz
piano/inst/extdata/probe2metabolites_iTO977.txt.gz
piano/inst/extdata/setup.txt
piano/man
piano/man/GSAheatmap.Rd
piano/man/GSAsummaryTable.Rd
piano/man/consensusHeatmap.Rd
piano/man/consensusScores.Rd
piano/man/diffExp.Rd
piano/man/extractFactors.Rd
piano/man/geneSetSummary.Rd
piano/man/gsa_input.Rd
piano/man/gsa_results.Rd
piano/man/loadGSC.Rd
piano/man/loadMAdata.Rd
piano/man/networkPlot.Rd
piano/man/piano-package.Rd
piano/man/polarPlot.Rd
piano/man/runGSA.Rd
piano/man/runGSAhyper.Rd
piano/man/runQC.Rd
piano/man/writeFilesForKiwi.Rd
piano/vignettes
piano/vignettes/consensus.png
piano/vignettes/diffexpfig.pdf
piano/vignettes/heatmap.pdf
piano/vignettes/naturenobf.bst
piano/vignettes/networkplot.pdf
piano/vignettes/networkplot2.pdf
piano/vignettes/piano-vignette.Rnw
piano/vignettes/qcfig.pdf
piano/vignettes/references.bib
piano/vignettes/rungsa.png