puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Bioconductor version: 3.24 · Package version: 3.55.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("puma")Details
| Maintainer | Xuejun Liu <xuejun.liu@nuaa.edu.cn> |
| Author | Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Guido Sanguinetti, Li Zhang |
| License | LGPL |
| URL | http://umber.sbs.man.ac.uk/resources/puma |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | AlternativeSplicing, Bayesian, ChipOnChip, Clustering, DataImport, DifferentialExpression, DifferentialSplicing, ExonArray, GeneExpression, HTA2.0, Microarray, OneChannel, Preprocessing, Software, TwoChannel, mRNAMicroarray |
| Package Short Url | https://bioconductor.org/packages/puma/ |
Citation
From within R, enter citation("puma"):
Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Guido Sanguinetti, Li Zhang. puma: Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0). doi:10.18129/B9.bioc.puma, R package version 3.55.0, https://bioconductor.org/packages/puma.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | puma_3.55.0.tar.gz |
| Windows binary (x86_64) | puma_3.55.0.zip |
| macOS binary (arm64) | puma_3.55.0.tgz |
| macOS binary (x86_64) | puma_3.55.0.tgz |
Dependencies
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