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'))

Peer review:

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

On CRAN:

6.53 score 9 stars 38 scripts 174 downloads 2 mentions 14 exports 38 dependencies

Last updated 4 years agofrom:08bf9c45d2. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-winNOTENov 01 2024
R-4.5-linuxNOTENov 01 2024
R-4.4-winNOTENov 01 2024
R-4.4-macNOTENov 01 2024
R-4.3-winNOTENov 01 2024
R-4.3-macNOTENov 01 2024

Exports:categorizedataCheckdoublesigmoidalFitFormuladoublesigmoidalFitFunctionfigureModelCurvesfitAndCategorizemultipleFitFunctionnormalizeDataparameterCalculationpreCategorizesameSourceDataChecksigmoidalFitFormulasigmoidalFitFunctionunnormalizeData

Dependencies:clicolorspacedplyrfansifarverfBasicsgenericsggplot2gluegssgtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvminpack.lmmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalesspatialstabledisttibbletidyselecttimeDatetimeSeriesutf8vctrsviridisLitewithr

Calculation of additional parameters of interest

Rendered fromadditional_parameters.Rmdusingknitr::rmarkdownon Nov 01 2024.

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

Fitting individual models

Rendered fromfitting_individual_models.Rmdusingknitr::rmarkdownon Nov 01 2024.

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

Identifying the best-fitting model category

Rendered fromcategorizing_fits.Rmdusingknitr::rmarkdownon Nov 01 2024.

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

Introduction

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 01 2024.

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

Plotting the fitted models

Rendered fromplotting_fitted_models.Rmdusingknitr::rmarkdownon Nov 01 2024.

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