timescape

DOI: 10.18129/B9.bioc.timescape    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see timescape.

Patient Clonal Timescapes

Bioconductor version: 3.8

TimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal prevalence vertically, time horizontally, and the plot height optionally encoding tumour volume during tumour-shrinking events. At each sampling time point (denoted by a faint white line), the height of each clone accurately reflects its proportionate prevalence. These prevalences form the anchors for bezier curves that visually represent the dynamic transitions between time points.

Author: Maia Smith [aut, cre]

Maintainer: Maia Smith <maiaannesmith at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("timescape")

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("timescape")

 

HTML	R Script	TimeScape vignette
PDF		Reference Manual
Text		README

Details

biocViews	BiomedicalInformatics, Software, Visualization
Version	1.6.0
In Bioconductor since	BioC 3.5 (R-3.4) (2 years)
License	GPL-3
Depends	R (>= 3.3)
Imports	htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), stringr (>= 1.0.0), dplyr (>= 0.4.3), gtools (>= 3.5.0)
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	timescape_1.6.0.tar.gz
Windows Binary	timescape_1.6.0.zip
Mac OS X 10.11 (El Capitan)	timescape_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/timescape
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/timescape
Package Short Url	http://bioconductor.org/packages/timescape/
Package Downloads Report	Download Stats