synergyfinder
This is the development version of synergyfinder; for the stable release version, see synergyfinder.
Calculate and Visualize Synergy Scores for Drug Combinations
Bioconductor version: Development (3.24)
Efficient implementations for analyzing pre-clinical multiple drug combination datasets. It provides efficient implementations for 1.the popular synergy scoring models, including HSA, Loewe, Bliss, and ZIP to quantify the degree of drug combination synergy; 2. higher order drug combination data analysis and synergy landscape visualization for unlimited number of drugs in a combination; 3. statistical analysis of drug combination synergy and sensitivity with confidence intervals and p-values; 4. synergy barometer for harmonizing multiple synergy scoring methods to provide a consensus metric of synergy; 5. evaluation of synergy and sensitivity simultaneously to provide an unbiased interpretation of the clinical potential of the drug combinations. Based on this package, we also provide a web application (http://www.synergyfinder.org) for users who prefer graphical user interface.
Author: Shuyu Zheng [aut, cre], Jing Tang [aut]
Maintainer: Shuyu Zheng <shuyu.zheng at helsinki.fi>
citation("synergyfinder")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("synergyfinder")
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("synergyfinder")| User tutorial of the SynergyFinder Plus | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Software, StatisticalMethod |
| Version | 3.21.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 years) |
| License | Mozilla Public License 2.0 |
| Depends | R (>= 4.0.0) |
| Imports | drc (>= 3.0-1), reshape2 (>= 1.4.4), tidyverse (>= 1.3.0), dplyr (>= 1.0.3), tidyr (>= 1.1.2), purrr (>= 0.3.4), furrr (>= 0.2.2), ggplot2 (>= 3.3.3), ggforce (>= 0.3.2), grid (>= 4.0.2), vegan (>= 2.5-7), gstat (>= 2.0-6), sp (>= 1.4-5), methods (>= 4.0.2), SpatialExtremes (>= 2.0-9), ggrepel (>= 0.9.1), kriging (>= 1.1), plotly (>= 4.9.3), stringr (>= 1.4.0), future (>= 1.21.0), mice (>= 3.13.0), lattice (>= 0.20-41), nleqslv (>= 3.3.2), stats (>= 4.0.2), graphics (>= 4.0.2), grDevices (>= 4.0.2), magrittr (>= 2.0.1), pbapply (>= 1.4-3), metR (>= 0.9.1) |
| System Requirements | |
| URL | http://www.synergyfinder.org |
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 | synergyfinder_3.21.0.tar.gz |
| Windows Binary (x86_64) | synergyfinder_3.21.0.zip |
| macOS Binary (big-sur-x86_64) | synergyfinder_3.21.0.tgz |
| macOS Binary (sonoma-arm64) | synergyfinder_3.21.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/synergyfinder |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/synergyfinder |
| Bioc Package Browser | https://code.bioconductor.org/browse/synergyfinder/ |
| Package Short Url | https://bioconductor.org/packages/synergyfinder/ |
| Package Downloads Report | Download Stats |