synergyfinder

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see synergyfinder.

Calculate and Visualize Synergy Scores for Drug Combinations


Bioconductor version: 3.13

Efficient implementations for analyzing pre-clinical multiple drug combination datasets. 1. Synergy scores valuculation via all the popular models, including HSA, Loewe, Bliss and ZIP; 2. Drug Sensitivity Score (CSS) and Relitave Inhibition (RI) for drug sensitivity evaluation; 3. Visualization for drug combination matrices and scores. Based on this package, we also provide a web application (https://synergyfinderplus.org/) for users who prefer more friendly user interface.

Author: Shuyu Zheng [aut, cre], Jing Tang [aut]

Maintainer: Shuyu Zheng <shuyu.zheng at helsinki.fi>

Citation (from within R, enter citation("synergyfinder")):

Installation

To install this package, start R (version "4.1") 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 PDF
NEWS Text

Details

biocViews Software, StatisticalMethod
Version 3.0.14
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_3.0.14.tar.gz
Windows Binary synergyfinder_3.0.14.zip (32- & 64-bit)
macOS 10.13 (High Sierra) synergyfinder_3.0.14.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 3.13 Source Archive