recipe bioconductor-iseetree

Interactive visualisation for microbiome data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/iSEEtree.html

License:

Artistic-2.0

Recipe:

/bioconductor-iseetree/meta.yaml

iSEEtree is an extension of iSEE for the TreeSummarizedExperiment. It leverages the functionality from the miaViz package for microbiome data visualisation to create panels that are specific for TreeSummarizedExperiment objects. Not surprisingly, it also depends on the generic panels from iSEE.

package bioconductor-iseetree

versions:

1.0.0-0

depends bioconductor-isee:

>=2.18.0,<2.19.0

depends bioconductor-mia:

>=1.14.0,<1.15.0

depends bioconductor-miaviz:

>=1.14.0,<1.15.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-treesummarizedexperiment:

>=2.14.0,<2.15.0

depends r-base:

>=4.4,<4.5.0a0

depends r-shiny:

depends r-shinywidgets:

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-iseetree

and update with::

   mamba update bioconductor-iseetree

To create a new environment, run:

mamba create --name myenvname bioconductor-iseetree

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-iseetree:<tag>

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

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