piano: Platform for integrative analysis of omics data
Version 1.16.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorLeif Varemo <piano.rpkg@gmail.com> and Intawat Nookaew <piano.rpkg@gmail.com>
Bioconductor views DifferentialExpression GeneExpression GeneSetEnrichment Microarray Pathways Preprocessing QualityControl Visualization
Date of publicationNone
MaintainerLeif Varemo <piano.rpkg@gmail.com>
LicenseGPL (>=2)
Version1.16.0
URL http://www.sysbio.se/piano
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("piano")

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

Functions

GSAheatmap Man page Source code
GSAsummaryTable Man page Source code
GSCsignificanceBatch Source code
GSCstatBatch Source code
GSCstatGenePerm Source code
GSCstatSamplePerm Source code
calcGeneSetStat Source code
checkLoadArg Source code
consensusHeatmap Man page Source code
consensusScores Man page Source code
diffExp Man page Source code
extractFactors Man page Source code
fdrGSEA Source code
geneSetSummary Man page Source code
gsa_input Man page
gsa_results Man page
loadGSC Man page Source code
loadMAdata Man page Source code
networkPlot Man page Source code
piano Man page
piano-package Man page
polarPlot Man page Source code
print.ArrayData Source code
print.GSAres Source code
print.GSC Source code
pvalFromDistribution Source code
pvalFromFractionGenePerm Source code
pvalFromFractionSamplePerm Source code
runGSA Man page Source code
runGSAhyper Man page Source code
runQC Man page Source code
writeFilesForKiwi Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GSAheatmap.R
R/GSAsummaryTable.R
R/GSCsignificanceBatch.R
R/GSCstatBatch.R
R/GSCstatGenePerm.R
R/GSCstatSamplePerm.R
R/calcGeneSetStat.R
R/checkLoadArg.r
R/consensusHeatmap.R
R/consensusScores.R
R/diffExp.r
R/extractFactors.r
R/fdrGSEA.R
R/geneSetSummary.R
R/loadGSC.R
R/loadMAdata.r
R/networkPlot.R
R/polarPlot.r
R/print_ArrayData.r
R/print_GSAres.R
R/print_GSC.R
R/pvalFromDistribution.R
R/pvalFromFractionGenePerm.R
R/pvalFromFractionSamplePerm.R
R/runGSA.r
R/runGSAhyper.R
R/runQC.r
R/writeFilesForKiwi.R
README.md
build
build/vignette.rds
data
data/gsa_input.RData
data/gsa_results.RData
inst
inst/CITATION
inst/doc
inst/doc/piano-vignette.R
inst/doc/piano-vignette.Rnw
inst/doc/piano-vignette.pdf
inst/extdata
inst/extdata/norm_data.txt.gz
inst/extdata/probe2metabolites_iIN800.txt.gz
inst/extdata/probe2metabolites_iTO977.txt.gz
inst/extdata/setup.txt
man
man/GSAheatmap.Rd
man/GSAsummaryTable.Rd
man/consensusHeatmap.Rd
man/consensusScores.Rd
man/diffExp.Rd
man/extractFactors.Rd
man/geneSetSummary.Rd
man/gsa_input.Rd
man/gsa_results.Rd
man/loadGSC.Rd
man/loadMAdata.Rd
man/networkPlot.Rd
man/piano-package.Rd
man/polarPlot.Rd
man/runGSA.Rd
man/runGSAhyper.Rd
man/runQC.Rd
man/writeFilesForKiwi.Rd
vignettes
vignettes/consensus.png
vignettes/diffexpfig.pdf
vignettes/heatmap.pdf
vignettes/naturenobf.bst
vignettes/networkplot.pdf
vignettes/networkplot2.pdf
vignettes/piano-vignette.Rnw
vignettes/qcfig.pdf
vignettes/references.bib
vignettes/rungsa.png
piano documentation built on May 20, 2017, 10:44 p.m.