synergyfinder

DOI: 10.18129/B9.bioc.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>

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")

 

HTML	R Script	User tutorial of the SynergyFinder Plus
PDF		Reference Manual
Text		NEWS

Details

biocViews	Software, StatisticalMethod
Version	3.4.5
In Bioconductor since	BioC 3.4 (R-3.3) (6 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)
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL	https://synergyfinderplus.org/
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	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
Package Short Url	https://bioconductor.org/packages/synergyfinder/
Package Downloads Report	Download Stats