piano
This is the development version of piano; for the stable release version, see piano.
Platform for integrative analysis of omics data
Bioconductor version: Development (3.24)
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("piano")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | R Script | |
| Running gene-set anaysis with piano | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, Microarray, Pathways, Preprocessing, QualityControl, Software, Visualization |
| Version | 2.29.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 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 |
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, SmartPhos |
| Suggests Me | BloodCancerMultiOmics2017 |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | piano_2.29.0.tar.gz |
| Windows Binary (x86_64) | piano_2.29.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | piano_2.29.0.tgz |
| macOS Binary (sonoma-arm64) | piano_2.29.0.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 |