recipe bioconductor-cancer

A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-cancer/meta.yaml

The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

package bioconductor-cancer

versions:

1.40.0-0,  1.36.0-0,  1.32.0-0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-cbioportaldata:

>=2.18.0,<2.19.0

depends bioconductor-genetclassifier:

>=1.46.0,<1.47.0

depends bioconductor-gseabase:

>=1.68.0,<1.69.0

depends bioconductor-phenotest:

>=1.54.0,<1.55.0

depends r-base:

>=4.4,<4.5.0a0

depends r-circlize:

depends r-dplyr:

depends r-formula:

depends r-plyr:

depends r-r.methodss3:

depends r-r.oo:

depends r-rpart:

depends r-runit:

depends r-survival:

depends r-tidyr:

depends r-tkrplot:

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-cancer

and update with::

   mamba update bioconductor-cancer

To create a new environment, run:

mamba create --name myenvname bioconductor-cancer

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-cancer:<tag>

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

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Link to this page

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