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

Bioconductor version: Release (3.19)

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.

Author: Shixiang Wang [aut, cre] , Maia Smith [aut]

Maintainer: Shixiang Wang <w_shixiang at>

Citation (from within R, enter citation("cellscape")):


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CellScape vignette HTML R Script
Reference Manual PDF


biocViews Software, Visualization
Version 1.28.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-3
Depends R (>= 3.3)
Imports dplyr (>= 0.4.3), gtools (>= 3.5.0), htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0)
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