recipe bioconductor-clipper

Gene Set Analysis Exploiting Pathway Topology

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/clipper.html

License:

AGPL-3

Recipe:

/bioconductor-clipper/meta.yaml

Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.

package bioconductor-clipper

versions:

1.40.0-0,  1.38.0-1,  1.38.0-0,  1.34.0-2,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0, 

1.40.0-0,  1.38.0-1,  1.38.0-0,  1.34.0-2,  1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.0-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-graph:

>=1.78.0,<1.79.0

depends bioconductor-kegggraph:

>=1.60.0,<1.61.0

depends bioconductor-qpgraph:

>=2.34.0,<2.35.0

depends bioconductor-rbgl:

>=1.76.0,<1.77.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-corpcor:

depends r-grbase:

>=1.6.6

depends r-igraph:

depends r-matrix:

depends r-rcpp:

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-clipper

and update with::

   mamba update bioconductor-clipper

To create a new environment, run:

mamba create --name myenvname bioconductor-clipper

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-clipper:<tag>

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

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