This is the released version of cellscape; for the devel version, see cellscape.
Explores single cell copy number profiles in the context of a single cell treeBioconductor version: Release (3.21)
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] ORCID: 0000-0001-9855-7357 , Maia Smith [aut]
Maintainer: Shixiang Wang <w_shixiang at 163.com>
Citation (from within R, entercitation("cellscape")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cellscape")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cellscape")Follow Installation instructions to use this package in your R session.
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