piano

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see piano.

Platform for integrative analysis of omics data

Bioconductor version: 3.21

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, Microarray, Pathways, Preprocessing, QualityControl, Software, Visualization

Version 2.24.0

In Bioconductor since BioC 2.12 (R-3.0) (12.5 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

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 cosmosR, BloodCancerMultiOmics2017

Links To Me

Build Report Build Report

Package Archives

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

Source Package piano_2.24.0.tar.gz

Windows Binary (x86_64) piano_2.24.0.zip

macOS Binary (x86_64) piano_2.24.0.tgz

macOS Binary (arm64) piano_2.24.0.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