DOI: 10.18129/B9.bioc.cellscape    

This is the development version of cellscape; for the stable release version, see cellscape.

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

Bioconductor version: Development (3.8)

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: Maia Smith [aut, cre]

Maintainer: Maia Smith <maiaannesmith at gmail.com>

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biocViews Software, Visualization
Version 1.5.0
In Bioconductor since BioC 3.5 (R-3.4) (1 year)
License GPL-3
Depends R (>= 3.3)
Imports htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0), plyr (>= 1.8.3), dplyr (>= 0.4.3), gtools (>= 3.5.0)
Suggests knitr, rmarkdown
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