piano

DOI: 10.18129/B9.bioc.piano  

Platform for integrative analysis of omics data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, Microarray, Pathways, Preprocessing, QualityControl, Software, Visualization
Version	2.14.0
In Bioconductor since	BioC 2.12 (R-3.0) (10 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
LinkingTo
Suggests	yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	http://www.sysbio.se/piano
BugReports	https://github.com/varemo/piano/issues
Depends On Me
Imports Me	CoreGx, PDATK
Suggests Me	BloodCancerMultiOmics2017, cosmosR
Links To Me
Build Report

Package Archives

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

Source Package	piano_2.14.0.tar.gz
Windows Binary	piano_2.14.0.zip
macOS Binary (x86_64)	piano_2.14.0.tgz
macOS Binary (arm64)	piano_2.14.0.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