Package: piano 2.29.0

Leif Varemo Wigge

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.

Authors:Leif Varemo Wigge <[email protected]> and Intawat Nookaew <[email protected]>

piano_2.29.0.tar.gz
piano_2.29.0.zip(r-4.7)piano_2.29.0.zip(r-4.6)piano_2.29.0.zip(r-4.5)
piano_2.29.0.tgz(r-4.6-any)piano_2.29.0.tgz(r-4.5-any)
piano_2.29.0.tar.gz(r-4.7-any)piano_2.29.0.tar.gz(r-4.6-any)
piano_2.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
piano/json (API)

# Install 'piano' in R:

install.packages('piano', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/varemo/piano/issues

Datasets:

gsa_input - Random input data for gene set analysis
gsa_results - Gene set analysis result data

On BioConductor:piano-2.29.0(bioc 3.24)piano-2.28.0(bioc 3.23)

microarray preprocessing qualitycontrol differentialexpression visualization geneexpression genesetenrichment pathways bioconductor bioconductor-package bioinformatics gene-set-enrichment transcriptomics

9.86 score 14 stars 9 packages 239 scripts 15 mentions 17 exports 86 dependencies

Last updated from:bccb63e8da. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	220
linux-devel-x86_64	NOTE	285
source / vignettes	OK	337
linux-release-x86_64	NOTE	288
macos-release-arm64	NOTE	146
macos-oldrel-arm64	NOTE	157
windows-devel	NOTE	233
windows-release	NOTE	268
windows-oldrel	NOTE	235
wasm-release	OK	208

Exports:consensusHeatmap consensusScores diffExp exploreGSAres extractFactors geneSetSummary GSAheatmap GSAsummaryTable loadGSC loadMAdata networkPlot networkPlot2 polarPlot runGSA runGSAhyper runQC writeFilesForKiwi

Dependencies:base64enc BH Biobase BiocGenerics BiocParallel bitops bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk data.table digest DT evaluate farver fastmap fastmatch fgsea fontawesome formatR fs futile.logger futile.options generics ggplot2 glue gplots gtable gtools highr htmltools htmlwidgets httpuv igraph isoband jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma magrittr marray Matrix memoise mime otel pkgconfig promises R6 rappdirs RColorBrewer Rcpp relations rlang rmarkdown S7 sass scales sets shiny shinydashboard shinyjs slam snow sourcetools statmod tinytex vctrs viridisLite visNetwork withr xfun xtable yaml

Running gene-set anaysis with piano

Quick start | Session info

Rendered fromRunning_gene-set_analysis_with_piano.Rmdusingknitr::rmarkdown

Last update: 2019-04-18
Started: 2019-04-17

Piano - Platform for Integrative Analysis of Omics data

Introduction | Getting started | Microarray analysis | Gene set analysis

Rendered frompiano-vignette.Rnwusingutils::Sweave

Last update: 2019-04-18
Started: 2013-04-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Piano - Platform for Integrative ANalysis of Omics data	piano-package piano
Heatmap of top consensus gene sets	consensusHeatmap
Top consensus gene sets and boxplot	consensusScores
Perform differential expression analysis	diffExp
Explore GSA results	exploreGSAres
Extracts 'ArrayData' factors	extractFactors
Gene set summary	geneSetSummary
Random input data for gene set analysis	gsa_input
Gene set analysis result data	gsa_results
Heatmap of top significant gene sets	GSAheatmap
Gene set analysis summary table	GSAsummaryTable
Load a gene set collection	loadGSC
Load and preprocess microarray data	loadMAdata
Gene set network plot	networkPlot
Gene set network plot	networkPlot2
Polar plot	polarPlot
Gene set analysis	runGSA
Gene set analysis with Fisher's exact test	runGSAhyper
Run quality control	runQC
Write files for Kiwi	writeFilesForKiwi