recipe bioconductor-svmdo

Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/SVMDO.html

License:

GPL-3

Recipe:

/bioconductor-svmdo/meta.yaml

It is an easy-to-use GUI using disease information for detecting tumor/normal sample discriminating gene sets from differentially expressed genes. Our approach is based on an iterative algorithm filtering genes with disease ontology enrichment analysis and wilk’s lambda criterion connected to SVM classification model construction. Along with gene set extraction, SVMDO also provides individual prognostic marker detection. The algorithm is designed for FPKM and RPKM normalized RNA-Seq transcriptome datasets.

package bioconductor-svmdo

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-dose:

>=3.28.0,<3.29.0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bsda:

>=1.2.1

depends r-caret:

>=6.0-93

depends r-catools:

>=1.18.2

depends r-data.table:

>=1.14.6

depends r-dplyr:

>=1.0.10

depends r-e1071:

>=1.7-12

depends r-golem:

>=0.3.5

depends r-klar:

>=1.7-1

depends r-nortest:

>=1.0-4

depends r-shiny:

>=1.7.4

depends r-shinyfiles:

>=0.9.3

depends r-shinytitle:

>=0.1.0

depends r-sjmisc:

>=2.8.9

depends r-survival:

>=3.4-0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-svmdo

and update with::

   mamba update bioconductor-svmdo

To create a new environment, run:

mamba create --name myenvname bioconductor-svmdo

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-svmdo/tags`_ for valid values for ``<tag>``)

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