recipe bioconductor-coregx

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

Homepage:

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

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

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-bumpymatrix >=1.6.0,<1.7.0

• bioconductor-matrixgenerics >=1.10.0,<1.11.0

• bioconductor-multiassayexperiment >=1.24.0,<1.25.0

• bioconductor-piano >=2.14.0,<2.15.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-bench

• r-checkmate

• r-crayon

• r-data.table

• r-glue

• r-lsa

• r-rlang

Required By:

• bioconductor-radiogx

• bioconductor-pharmacogx

• bioconductor-toxicogx

• bioconductor-pdatk

Installation

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

conda install bioconductor-coregx

and update with:

conda update bioconductor-coregx

or 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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