recipe bioconductor-cellscape

Explores single cell copy number profiles in the context of a single cell tree






CellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of source-target edges to support arbitrary representations, where each node may or may not have associated genomic data. The output of CellScape is an interactive interface displaying a single cell phylogeny and a cell-by-locus genomic heatmap representing the mutation status in each cell for each locus.

package bioconductor-cellscape

(downloads) docker_bioconductor-cellscape



depends r-base:


depends r-dplyr:


depends r-gtools:


depends r-htmlwidgets:


depends r-jsonlite:


depends r-plyr:


depends r-reshape2:


depends r-stringr:




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-cellscape

and update with::

   mamba update bioconductor-cellscape

To create a new environment, run:

mamba create --name myenvname bioconductor-cellscape

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

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