timescape
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see timescape.
Patient Clonal Timescapes
Bioconductor version: 3.9
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>
citation("timescape")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| TimeScape vignette | HTML | R Script |
| Reference Manual | ||
| README | Text |
Details
| biocViews | BiomedicalInformatics, Software, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 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) |
| 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 | timescape_1.8.0.tar.gz |
| Windows Binary | timescape_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | timescape_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/timescape |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/timescape |
| Bioc Package Browser | https://code.bioconductor.org/browse/timescape/ |
| Package Short Url | https://bioconductor.org/packages/timescape/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |