recipe bioconductor-iseepathways

iSEE extension for panels related to pathway analysis






This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.

package bioconductor-iseepathways

(downloads) docker_bioconductor-iseepathways



depends bioconductor-isee:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-ggplot2:

depends r-shiny:

depends r-shinywidgets:



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-iseepathways

and update with::

   mamba update bioconductor-iseepathways

To create a new environment, run:

mamba create --name myenvname bioconductor-iseepathways

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<tag>

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

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