recipe bioconductor-desubs

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-desubs/meta.yaml

DEsubs is a network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customizable framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render it a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level biomarkers for complex diseases.

package bioconductor-desubs

versions:

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.1-1, 

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.1-1,  1.8.1-0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-ebseq:

>=2.0.0,<2.1.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-rbgl:

>=1.78.0,<1.79.0

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-ggplot2:

depends r-igraph:

depends r-jsonlite:

depends r-locfit:

depends r-matrix:

depends r-nbpseq:

depends r-pheatmap:

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-desubs

and update with::

   mamba update bioconductor-desubs

To create a new environment, run:

mamba create --name myenvname bioconductor-desubs

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-desubs:<tag>

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

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