Package: sicegar 0.2.4

Claus O. Wilke

sicegar: Analysis of Single-Cell Viral Growth Curves

Aims to quantify time intensity data by using sigmoidal and double sigmoidal curves. It fits straight lines, sigmoidal, and double sigmoidal curves on to time vs intensity data. Then all the fits are used to make decision on which model best describes the data. This method was first developed in the context of single-cell viral growth analysis (for details, see Caglar et al. (2018) <doi:10.7717/peerj.4251>), and the package name stands for "SIngle CEll Growth Analysis in R".

Authors:M. Umut Caglar [aut], Claus O. Wilke [aut, cre]

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sicegar.pdf |sicegar.html
sicegar/json (API)

# Install 'sicegar' in R:
install.packages('sicegar', repos = c('https://wilkelab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wilkelab/sicegar/issues

On CRAN:

Conda:

6.57 score 9 stars 41 scripts 189 downloads 2 mentions 14 exports 38 dependencies

Last updated 4 years agofrom:08bf9c45d2. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 31 2025
R-4.5-winNOTEMar 31 2025
R-4.5-macNOTEMar 31 2025
R-4.5-linuxNOTEMar 31 2025
R-4.4-winNOTEMar 31 2025
R-4.4-macNOTEMar 31 2025
R-4.4-linuxNOTEMar 31 2025
R-4.3-winNOTEMar 31 2025
R-4.3-macNOTEMar 31 2025

Exports:categorizedataCheckdoublesigmoidalFitFormuladoublesigmoidalFitFunctionfigureModelCurvesfitAndCategorizemultipleFitFunctionnormalizeDataparameterCalculationpreCategorizesameSourceDataChecksigmoidalFitFormulasigmoidalFitFunctionunnormalizeData

Dependencies:clicolorspacedplyrfansifarverfBasicsgenericsggplot2gluegssgtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvminpack.lmmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalesspatialstabledisttibbletidyselecttimeDatetimeSeriesutf8vctrsviridisLitewithr

Calculation of additional parameters of interest

Rendered fromadditional_parameters.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2017-07-11
Started: 2017-06-22

Fitting individual models

Rendered fromfitting_individual_models.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2017-07-11
Started: 2017-06-23

Identifying the best-fitting model category

Rendered fromcategorizing_fits.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2017-07-28
Started: 2017-06-23

Introduction

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2019-08-22
Started: 2017-06-21

Plotting the fitted models

Rendered fromplotting_fitted_models.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2017-07-11
Started: 2017-06-23