puma

DOI: 10.18129/B9.bioc.puma  

Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Bioconductor version: Release (3.16)

Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.

Author: Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Guido Sanguinetti, Li Zhang

Maintainer: Xuejun Liu <xuejun.liu at nuaa.edu.cn>

Installation

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

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

BiocManager::install("puma")

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("puma")

 

PDF	R Script	puma User Guide
PDF		Reference Manual

Details

biocViews	AlternativeSplicing, Bayesian, ChipOnChip, Clustering, DataImport, DifferentialExpression, DifferentialSplicing, ExonArray, GeneExpression, HTA2.0, Microarray, OneChannel, Preprocessing, Software, TwoChannel, mRNAMicroarray
Version	3.40.0
In Bioconductor since	BioC 2.0 (R-2.5) (16 years)
License	LGPL
Depends	R (>= 3.2.0), oligo(>= 1.32.0), graphics, grDevices, methods, stats, utils, mclust, oligoClasses
Imports	Biobase(>= 2.5.5), affy(>= 1.46.0), affyio, oligoClasses
LinkingTo
Suggests	pumadata, affydata, snow, limma, ROCR, annotate
SystemRequirements
Enhances
URL	http://umber.sbs.man.ac.uk/resources/puma
Depends On Me	pumadata
Imports Me
Suggests Me	tigre
Links To Me
Build Report

Package Archives

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

Source Package	puma_3.40.0.tar.gz
Windows Binary	puma_3.40.0.zip (64-bit only)
macOS Binary (x86_64)	puma_3.40.0.tgz
macOS Binary (arm64)	puma_3.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/puma
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/puma
Bioc Package Browser	https://code.bioconductor.org/browse/puma/
Package Short Url	https://bioconductor.org/packages/puma/
Package Downloads Report	Download Stats