To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R") biocLite("puma")
In most cases, you don't need to download the package archive at all.
Bioconductor version: 2.14
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: Richard Pearson <richard.pearson at well.ox.ac.uk>
Citation (from within R,
enter citation("puma")
):
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R") biocLite("puma")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("puma")
Reference Manual |
biocViews | Bioinformatics, Clustering, DifferentialExpression, Microarray, OneChannel, Preprocessing, Software |
Version | 3.6.0 |
In Bioconductor since | BioC 2.0 (R-2.5) |
License | LGPL |
Depends | R (>= 3.0), Biobase(>= 2.5.5), affy(>= 1.41.3), graphics, grDevices, methods, stats, utils, mclust, oligo |
Imports | Biobase(>= 2.5.5), affy(>= 1.41.3), affyio |
Suggests | pumadata, affydata, snow, limma, ROCR, annotate |
System Requirements | |
URL | http://umber.sbs.man.ac.uk/resources/puma |
Depends On Me | pumadata |
Imports Me | tigre |
Suggests Me |
Follow Installation instructions to use this package in your R session.
Package Source | puma_3.6.0.tar.gz |
Windows Binary | puma_3.6.0.zip (32- & 64-bit) |
Mac OS X 10.6 (Snow Leopard) | puma_3.6.0.tgz |
Mac OS X 10.9 (Mavericks) | puma_3.6.0.tgz |
Browse/checkout source | (username/password: readonly) |
Package Downloads Report | Download Stats |
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