r-sbpiper

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Provides an API for analysing repetitive parameter estimations and simulations of mathematical models. Examples of mathematical models are Ordinary Differential equations (ODEs) or Stochastic Differential Equations (SDEs) models. Among the analyses for parameter estimation ‘sbpiper’ calculates statistics and generates plots for parameter density, PCA of the best fits, parameter profile likelihood estimations (PLEs), and 2D parameter PLEs. These results can be generated using all or a subset of the best computed parameter sets. Among the analyses for model simulation ‘sbpiper’ calculates statistics and generates plots for deterministic and stochastic time courses via cartesian and heatmap plots. Plots for the scan of one or two model parameters can also be generated. This package is primarily used by the software ‘SBpipe’. Citation: Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology. 2017;11:46. <doi:10.1186/s12918-017-0423-3>.

Home https://github.com/pdp10/sbpiper
Versions 1.9.0, 1.8.0
License MIT
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/r-sbpiper
Links doi: 10.1186/s12918-017-0423-3

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install r-sbpiper

and update with:

conda update r-sbpiper

docker

A Docker container is available at https://quay.io/repository/biocontainers/r-sbpiper.