puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Bioconductor version: Release (3.17)
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>
citation("puma")):
Installation
To install this package, start R (version "4.3") 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")| puma User Guide | R Script | |
| Reference Manual |
Details
| biocViews | AlternativeSplicing, Bayesian, ChipOnChip, Clustering, DataImport, DifferentialExpression, DifferentialSplicing, ExonArray, GeneExpression, HTA2.0, Microarray, OneChannel, Preprocessing, Software, TwoChannel, mRNAMicroarray |
| Version | 3.42.0 |
| In Bioconductor since | BioC 2.0 (R-2.5) (16.5 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 |
| Linking To | |
| Suggests | pumadata, affydata, snow, limma, ROCR, annotate |
| System Requirements | |
| Enhances | |
| URL | http://umber.sbs.man.ac.uk/resources/puma |
See More
| 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_3.42.0.tar.gz |
| Windows Binary | puma_3.42.0.zip |
| macOS Binary (x86_64) | puma_3.42.0.tgz |
| macOS Binary (arm64) | puma_3.42.0.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 |