recipe bioconductor-survclust

Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/survClust.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-survclust/meta.yaml

survClust is an outcome weighted integrative clustering algorithm used to classify multi-omic samples on their available time to event information. The resulting clusters are cross-validated to avoid over overfitting and output classification of samples that are molecularly distinct and clinically meaningful. It takes in binary (mutation) as well as continuous data (other omic types).

package bioconductor-survclust

versions:

1.0.0-0

depends bioconductor-multiassayexperiment:

>=1.32.0,<1.33.0

depends bioconductor-multiassayexperiment:

>=1.32.0,<1.33.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-pdist:

depends r-rcpp:

depends r-survival:

requirements:

additional platforms:

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-survclust

and update with::

   mamba update bioconductor-survclust

To create a new environment, run:

mamba create --name myenvname bioconductor-survclust

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-survclust:<tag>

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

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