piano: Platform for integrative analysis of omics data

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.

AuthorLeif Varemo <piano.rpkg@gmail.com> and Intawat Nookaew <piano.rpkg@gmail.com>
Date of publicationNone
MaintainerLeif Varemo <piano.rpkg@gmail.com>
LicenseGPL (>=2)
Version1.14.5
http://www.sysbio.se/piano

View on Bioconductor

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

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