recipe bioconductor-clipper

Gene Set Analysis Exploiting Pathway Topology

Homepage:

https://bioconductor.org/packages/3.16/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:

1.38.0-1,  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, 

1.38.0-1,  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 >=2.58.0,<2.59.0

• bioconductor-graph >=1.76.0,<1.77.0

• bioconductor-kegggraph >=1.58.0,<1.59.0

• bioconductor-qpgraph >=2.32.0,<2.33.0

• bioconductor-rbgl >=1.74.0,<1.75.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-corpcor

• r-grbase >=1.6.6

• r-igraph

• r-matrix

• r-rcpp

Required By:

Installation

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

conda install bioconductor-clipper

and update with:

conda update bioconductor-clipper

or use the docker container:

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

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

Download stats

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