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## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cellscape")

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cellscape

DOI: 10.18129/B9.bioc.cellscape    

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

Bioconductor version: Release (3.5)

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

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Details

biocViews Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
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

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Package Source 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/
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