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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cellscape")
In most cases, you don't need to download the package archive at all.
cellscape
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Explores single cell copy number profiles in the context of a single cell tree
Bioconductor version: Release (3.5)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cellscape")
Documentation
| HTML | R Script | CellScape vignette |
| Reference Manual |
Details
| biocViews | Software, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (0.5 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cellscape_1.0.0.tar.gz |
| Windows Binary | cellscape_1.0.0.zip |
| Mac OS X 10.11 (El Capitan) | cellscape_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cellscape |
| Package Short Url | http://bioconductor.org/packages/cellscape/ |
| Package Downloads Report | Download Stats |
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