recipe bioconductor-cimice

CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution






CIMICE is a tool in the field of tumor phylogenetics and its goal is to build a Markov Chain (called Cancer Progression Markov Chain, CPMC) in order to model tumor subtypes evolution. The input of CIMICE is a Mutational Matrix, so a boolean matrix representing altered genes in a collection of samples. These samples are assumed to be obtained with single-cell DNA analysis techniques and the tool is specifically written to use the peculiarities of this data for the CMPC construction.

package bioconductor-cimice

(downloads) docker_bioconductor-cimice



depends bioconductor-maftools:


depends r-assertthat:

depends r-base:


depends r-dplyr:

depends r-expm:

depends r-ggcorrplot:

depends r-ggplot2:

depends r-ggraph:

depends r-glue:

depends r-igraph:

depends r-matrix:

depends r-networkd3:

depends r-purrr:

depends r-tidygraph:

depends r-tidyr:

depends r-visnetwork:



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-cimice

and update with::

   mamba update bioconductor-cimice

To create a new environment, run:

mamba create --name myenvname bioconductor-cimice

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

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