recipe bioconductor-synergyfinder

Calculate and Visualize Synergy Scores for Drug Combinations

Homepage:

https://bioconductor.org/packages/3.17/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:

3.10.0-0,  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, 

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 r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

>=1.0.3

depends r-drc:

>=3.0-1

depends r-furrr:

>=0.2.2

depends r-future:

>=1.21.0

depends r-ggforce:

>=0.3.2

depends r-ggplot2:

>=3.3.3

depends r-ggrepel:

>=0.9.1

depends r-gstat:

>=2.0-6

depends r-kriging:

>=1.1

depends r-lattice:

>=0.20-41

depends r-magrittr:

>=2.0.1

depends r-metr:

>=0.9.1

depends r-mice:

>=3.13.0

depends r-nleqslv:

>=3.3.2

depends r-pbapply:

>=1.4-3

depends r-plotly:

>=4.9.3

depends r-purrr:

>=0.3.4

depends r-reshape2:

>=1.4.4

depends r-sp:

>=1.4-5

depends r-spatialextremes:

>=2.0-9

depends r-stringr:

>=1.4.0

depends r-tidyr:

>=1.1.2

depends r-tidyverse:

>=1.3.0

depends r-vegan:

>=2.5-7

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-synergyfinder

and update with::

   mamba update bioconductor-synergyfinder

To create a new environment, run:

mamba create --name myenvname bioconductor-synergyfinder

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

Download stats

Link to this page

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