Package Recipe 'bioconductor-synergyfinder'

recipe bioconductor-synergyfinder

Calculate and Visualize Synergy Scores for Drug Combinations

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/synergyfinder.html
License:: Mozilla Public License 2.0
Recipe:: /bioconductor-synergyfinder/meta.yaml
Links:: biotools: synergyfinder, doi: 10.1093/bioinformatics/btx162

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.

package bioconductor-synergyfinder¶

Versions:

3.18.0-0, 3.14.0-0, 3.10.0-0, 3.8.2-0, 3.6.0-0, 3.2.2-0, 3.0.3-0, 2.4.10-0, 2.4.0-0,

3.18.0-0, 3.14.0-0, 3.10.0-0, 3.8.2-0, 3.6.0-0, 3.2.2-0, 3.0.3-0, 2.4.10-0, 2.4.0-0, 2.2.0-0, 2.0.1-0, 1.10.2-0, 1.10.0-0, 1.8.0-0, 1.6.1-0, 1.4.0-0, 1.2.0-0, 1.0.0-0

Depends:

on r-base >=4.5,<4.6.0a0
on r-dplyr >=1.0.3
on r-drc >=3.0-1
on r-furrr >=0.2.2
on r-future >=1.21.0
on r-ggforce >=0.3.2
on r-ggplot2 >=3.3.3
on r-ggrepel >=0.9.1
on r-gstat >=2.0-6
on r-kriging >=1.1
on r-lattice >=0.20-41
on r-magrittr >=2.0.1
on r-metr >=0.9.1
on r-mice >=3.13.0
on r-nleqslv >=3.3.2
on r-pbapply >=1.4-3
on r-plotly >=4.9.3
on r-purrr >=0.3.4
on r-reshape2 >=1.4.4
on r-sp >=1.4-5
on r-spatialextremes >=2.0-9
on r-stringr >=1.4.0
on r-tidyr >=1.1.2
on r-tidyverse >=1.3.0
on r-vegan >=2.5-7

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-synergyfinder

to add into an existing workspace instead, run:

pixi add bioconductor-synergyfinder

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-synergyfinder

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-synergyfinder

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-synergyfinder:<tag>

(see bioconductor-synergyfinder/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-synergyfinder/README.html)