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 (3.21)
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:
Maintainer: Shixiang Wang <w_shixiang at 163.com>
citation("cellscape")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
biocViews | Software, Visualization |
Version | 1.31.0 |
In Bioconductor since | BioC 3.5 (R-3.4) (7.5 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_1.31.0.tar.gz |
Windows Binary (x86_64) | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
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 |