recipe bioconductor-rscudo

Signature-based Clustering for Diagnostic Purposes

Homepage

https://bioconductor.org/packages/3.14/bioc/html/rScudo.html

License

GPL-3

Recipe

/bioconductor-rscudo/meta.yaml

SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. It is based on the identification of sample-specific gene signatures composed of the most up- and down-regulated genes for that sample. Starting from gene expression data, functions in this package identify sample-specific gene signatures and use them to build a graph of samples. In this graph samples are joined by edges if they have a similar expression profile, according to a pre-computed similarity matrix. The similarity between the expression profiles of two samples is computed using a method similar to GSEA. The graph of samples can then be used to perform community clustering or to perform supervised classification of samples in a testing set.

package bioconductor-rscudo

Versions

1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

Depends

• bioconductor-biobase >=2.54.0,<2.55.0

• bioconductor-biocgenerics >=0.40.0,<0.41.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• r-base >=4.1,<4.2.0a0

• r-igraph

• r-stringr

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-rscudo

and update with:

conda update bioconductor-rscudo

or use the docker container:

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

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

Download stats

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