clevRvis
This is the released version of clevRvis; for the devel version, see clevRvis.
Visualization Techniques for Clonal Evolution
Bioconductor version: Release (3.23)
clevRvis provides a set of visualization techniques for clonal evolution. These include shark plots, dolphin plots and plaice plots. Algorithms for time point interpolation as well as therapy effect estimation are provided. Phylogeny-aware color coding is implemented. A shiny-app for generating plots interactively is additionally provided.
Author: Sarah Sandmann [aut, cre]
Maintainer: Sarah Sandmann <sarah.sandmann at uni-muenster.de>
citation("clevRvis")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("clevRvis")
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("clevRvis")| ClEvR Viz vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ShinyApps, Software, Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | LGPL-3 |
| Depends | |
| Imports | shiny, ggraph, igraph, ggiraph, cowplot, htmlwidgets, readxl, dplyr, readr, purrr, tibble, patchwork, R.utils, shinyWidgets, colorspace, shinyhelper, shinycssloaders, ggnewscale, shinydashboard, DT, colourpicker, grDevices, methods, utils, stats, ggplot2, magrittr, tools |
| System Requirements | |
| URL | https://github.com/sandmanns/clevRvis |
| Bug Reports | https://github.com/sandmanns/clevRvis/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| 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 | clevRvis_1.12.0.tar.gz |
| Windows Binary (x86_64) | clevRvis_1.12.0.zip |
| macOS Binary (big-sur-x86_64) | clevRvis_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | clevRvis_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/clevRvis |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/clevRvis |
| Bioc Package Browser | https://code.bioconductor.org/browse/clevRvis/ |
| Package Short Url | https://bioconductor.org/packages/clevRvis/ |
| Package Downloads Report | Download Stats |