recipe bioconductor-coregx

Classes and Functions to Serve as the Basis for Other 'Gx' Packages

Homepage:

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

License:

GPL (>= 3)

Recipe:

/bioconductor-coregx/meta.yaml

A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmacoSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.

package bioconductor-coregx

versions:

2.6.0-0,  2.4.0-0,  2.2.0-0,  1.6.0-0,  1.4.1-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-bumpymatrix:

>=1.10.0,<1.11.0

depends bioconductor-matrixgenerics:

>=1.14.0,<1.15.0

depends bioconductor-multiassayexperiment:

>=1.28.0,<1.29.0

depends bioconductor-piano:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bench:

depends r-checkmate:

depends r-crayon:

depends r-data.table:

depends r-glue:

depends r-lsa:

depends r-rlang:

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-coregx

and update with::

   mamba update bioconductor-coregx

To create a new environment, run:

mamba create --name myenvname bioconductor-coregx

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-coregx:<tag>

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

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