recipe bioconductor-radiogx

Analysis of Large-Scale Radio-Genomic Data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-radiogx/meta.yaml

Computational tool box for radio-genomic analysis which integrates radio-response data, radio-biological modelling and comprehensive cell line annotations for hundreds of cancer cell lines. The 'RadioSet' class enables creation and manipulation of standardized datasets including information about cancer cells lines, radio-response assays and dose-response indicators. Included methods allow fitting and plotting dose-response data using established radio-biological models along with quality control to validate results. 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, references, as well as: Manem, V. et al (2018) <doi:10.1101/449793>.

package bioconductor-radiogx

versions:

2.10.0-0,  2.6.0-0,  2.4.0-0,  2.2.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-coregx:

>=2.10.0,<2.11.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-assertthat:

depends r-base:

>=4.4,<4.5.0a0

depends r-catools:

depends r-data.table:

depends r-downloader:

depends r-magicaxis:

depends r-matrixstats:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-scales:

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-radiogx

and update with::

   mamba update bioconductor-radiogx

To create a new environment, run:

mamba create --name myenvname bioconductor-radiogx

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-radiogx:<tag>

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

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