synergyfinder
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see synergyfinder.
Calculate and Visualize Synergy Scores for Drug Combinations
Bioconductor version: 3.15
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 (https://synergyfinderplus.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")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 3.4.5 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 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 | https://synergyfinderplus.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_3.4.5.tar.gz |
| Windows Binary | synergyfinder_3.4.5.zip |
| macOS Binary (x86_64) | synergyfinder_3.4.5.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 |
| Old Source Packages for BioC 3.15 | Source Archive |