Welcome to the new bioconductor.org!

cellscape

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


Bioconductor version: Release (3.18)

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 163.com>

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

Installation

To install this package, start R (version "4.3") 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 1.26.0
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)
System Requirements
URL
See More
Suggests knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package cellscape_1.26.0.tar.gz
Windows Binary cellscape_1.26.0.zip
macOS Binary (x86_64) cellscape_1.26.0.tgz
macOS Binary (arm64) cellscape_1.26.0.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