synergyfinder

DOI: 10.18129/B9.bioc.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 (3.14)

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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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")

 

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

Details

biocViews Software, StatisticalMethod
Version 3.1.15
In Bioconductor since BioC 3.4 (R-3.3) (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)
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_3.1.15.tar.gz
Windows Binary synergyfinder_3.1.15.zip
macOS 10.13 (High Sierra) synergyfinder_3.1.15.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

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