recipe bioconductor-netdx

Network-based patient classifier

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-netdx/meta.yaml

netDx is a general-purpose algorithm to build a patient classifier from heterogenous patient data. The method converts data into patient similarity networks at the level of features. Feature selection identifies features of predictive value to each class. Methods are provided for versatile predictor design and performance evaluation using standard measures. netDx natively groups molecular data into pathway-level features and connects with Cytoscape for network visualization of pathway themes. For method details see: Pai et al. (2019). netDx: interpretable patient classification using integrated patient similarity networks. Molecular Systems Biology. 15, e8497

package bioconductor-netdx

versions:

1.14.0-0,  1.12.0-0,  1.9.0-0,  1.6.0-0,  1.4.0-0,  1.2.2-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-multiassayexperiment:

>=1.28.0,<1.29.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bigmemory:

depends r-combinat:

depends r-doparallel:

depends r-foreach:

depends r-ggplot2:

depends r-glmnet:

depends r-httr:

depends r-igraph:

depends r-plotrix:

depends r-pracma:

depends r-rappdirs:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rocr:

depends r-rtsne:

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-netdx

and update with::

   mamba update bioconductor-netdx

To create a new environment, run:

mamba create --name myenvname bioconductor-netdx

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-netdx:<tag>

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

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