cellscape

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see cellscape.

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


Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") 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")
CellScape vignette HTML R Script
Reference Manual PDF

Details

biocViews Software, Visualization
Version 1.8.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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)
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Package Archives

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

Source Package cellscape_1.8.0.tar.gz
Windows Binary cellscape_1.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) cellscape_1.8.0.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
Old Source Packages for BioC 3.9 Source Archive