cellscape

DOI: 10.18129/B9.bioc.cellscape  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cellscape")

 

HTML	R Script	CellScape vignette
PDF		Reference Manual

Details

biocViews	Software, Visualization
Version	1.22.0
In Bioconductor since	BioC 3.5 (R-3.4) (6 years)
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)
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	cellscape_1.22.0.tar.gz
Windows Binary	cellscape_1.22.0.zip
macOS Binary (x86_64)	cellscape_1.22.0.tgz
macOS Binary (arm64)	cellscape_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cellscape
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cellscape
Bioc Package Browser	https://code.bioconductor.org/browse/cellscape/
Package Short Url	https://bioconductor.org/packages/cellscape/
Package Downloads Report	Download Stats