recipe bioconductor-toxicogx

Analysis of Large-Scale Toxico-Genomic Data

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-toxicogx/meta.yaml

Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data.

package bioconductor-toxicogx

versions:

2.6.0-0,  2.4.0-0,  2.2.0-0,  1.4.0-0,  1.2.0-0,  1.0.1-0,  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-coregx:

>=2.6.0,<2.7.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-catools:

depends r-data.table:

depends r-downloader:

depends r-dplyr:

depends r-ggplot2:

depends r-jsonlite:

depends r-magrittr:

depends r-reshape2:

depends r-scales:

depends r-tibble:

depends r-tidyr:

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-toxicogx

and update with::

   mamba update bioconductor-toxicogx

To create a new environment, run:

mamba create --name myenvname bioconductor-toxicogx

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-toxicogx:<tag>

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

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Link to this page

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