recipe bioconductor-puma

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

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/puma.html

License:

LGPL

Recipe:

/bioconductor-puma/meta.yaml

Links:

biotools: puma

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.

package bioconductor-puma

Versions:

3.40.0-0,  3.36.0-2,  3.36.0-1,  3.36.0-0,  3.34.0-0,  3.32.0-1,  3.32.0-0,  3.30.0-0,  3.28.0-0, 

3.40.0-0,  3.36.0-2,  3.36.0-1,  3.36.0-0,  3.34.0-0,  3.32.0-1,  3.32.0-0,  3.30.0-0,  3.28.0-0,  3.26.0-1,  3.24.0-0,  3.22.0-0,  3.20.0-0

Depends:

• bioconductor-affy >=1.76.0,<1.77.0

• bioconductor-affyio >=1.68.0,<1.69.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-oligo >=1.62.0,<1.63.0

• bioconductor-oligoclasses >=1.60.0,<1.61.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• r-base >=4.2,<4.3.0a0

• r-mclust

Required By:

• bioconductor-pumadata

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-puma

and update with:

conda update bioconductor-puma

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-puma:<tag>

(see bioconductor-puma/tags for valid values for <tag>)

Download stats

Link to this page

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