recipe bioconductor-setools

SEtools: tools for working with SummarizedExperiment

Homepage:

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

License:

GPL

Recipe:

/bioconductor-setools/meta.yaml

This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details).

package bioconductor-setools

versions:

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-sechm:

>=1.10.0,<1.11.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-sva:

>=3.50.0,<3.51.0

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-data.table:

depends r-matrix:

depends r-openxlsx:

depends r-pheatmap:

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-setools

and update with::

   mamba update bioconductor-setools

To create a new environment, run:

mamba create --name myenvname bioconductor-setools

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-setools:<tag>

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

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