Package Recipe 'bioconductor-coregx'

recipe bioconductor-coregx

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

Homepage:: https://bioconductor.org/packages/3.20/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:

2.14.0-0, 2.10.0-0, 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,

2.14.0-0, 2.10.0-0, 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:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-bumpymatrix >=1.18.0,<1.19.0
on bioconductor-matrixgenerics >=1.22.0,<1.23.0
on bioconductor-multiassayexperiment >=1.36.0,<1.37.0
on bioconductor-piano >=2.26.0,<2.27.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-bench
on r-checkmate
on r-crayon
on r-data.table
on r-glue
on r-lsa
on r-rlang

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-coregx

to add into an existing workspace instead, run:

pixi add bioconductor-coregx

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-coregx

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-coregx

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-coregx:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-coregx/README.html)