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piano

Platform for integrative analysis of omics data


Bioconductor version: Release (3.18)

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 Wigge <piano.rpkg at gmail.com> and Intawat Nookaew <piano.rpkg at gmail.com>

Maintainer: Leif Varemo Wigge <piano.rpkg at gmail.com>

Citation (from within R, enter citation("piano")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("piano")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("piano")
Piano - Platform for Integrative Analysis of Omics data PDF R Script
Running gene-set anaysis with piano HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, Microarray, Pathways, Preprocessing, QualityControl, Software, Visualization
Version 2.18.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License GPL (>=2)
Depends R (>= 3.5)
Imports BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods
System Requirements
URL http://www.sysbio.se/piano
Bug Reports https://github.com/varemo/piano/issues
See More
Suggests yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me CoreGx, PDATK
Suggests Me BloodCancerMultiOmics2017, cosmosR
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package piano_2.18.0.tar.gz
Windows Binary piano_2.18.0.zip (64-bit only)
macOS Binary (x86_64) piano_2.18.0.tgz
macOS Binary (arm64) piano_2.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/piano
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/piano
Bioc Package Browser https://code.bioconductor.org/browse/piano/
Package Short Url https://bioconductor.org/packages/piano/
Package Downloads Report Download Stats