recipe bioconductor-autonomics

Generifying and intuifying cross-platform omics analysis

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-autonomics/meta.yaml

This package offers a generic and intuitive solution for cross-platform omics data analysis. It has functions for import, preprocessing, exploration, contrast analysis and visualization of omics data. It follows a tidy, functional programming paradigm.

package bioconductor-autonomics

versions:

1.10.2-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-multiassayexperiment:

>=1.28.0,<1.29.0

depends bioconductor-pcamethods:

>=1.94.0,<1.95.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-abind:

depends r-assertive.base:

depends r-assertive.files:

depends r-assertive.numbers:

depends r-assertive.sets:

depends r-base:

>=4.3,<4.4.0a0

depends r-bit64:

depends r-colorspace:

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-ggrepel:

depends r-gridextra:

depends r-magrittr:

depends r-matrixstats:

depends r-r.utils:

depends r-rappdirs:

depends r-readxl:

depends r-rlang:

depends r-scales:

depends r-stringi:

depends r-tidyr:

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-autonomics

and update with::

   mamba update bioconductor-autonomics

To create a new environment, run:

mamba create --name myenvname bioconductor-autonomics

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-autonomics:<tag>

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

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Link to this page

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