recipe bioconductor-assign

Adaptive Signature Selection and InteGratioN (ASSIGN)






ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literature or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.

package bioconductor-assign

(downloads) docker_bioconductor-assign



depends bioconductor-sva:


depends r-base:


depends r-ggplot2:

depends r-gplots:

depends r-msm:

depends r-rlab:

depends r-yaml:



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-assign

and update with::

   mamba update bioconductor-assign

To create a new environment, run:

mamba create --name myenvname bioconductor-assign

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-assign/tags`_ for valid values for ``<tag>``)

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