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".

Version: 0.3.0
Imports: minpack.lm, fBasics, ggplot2, stats, dplyr
Suggests: covr, cowplot, testthat, knitr, rmarkdown
Published: 2025-11-15
DOI: 10.32614/CRAN.package.sicegar
Author: Johanna Hardin ORCID iD [aut, cre], Samuel Butler [aut], Phineus Choi [aut], Thomas Matheis [aut], Mira Terdiman [aut], M. Umut Caglar [aut], Claus O. Wilke ORCID iD [aut]
Maintainer: Johanna Hardin <jo.hardin at pomona.edu>
BugReports: https://github.com/hardin47/sicegar/issues
License: GPL-2 | GPL-3
URL: https://github.com/wilkelab/sicegar/, https://hardin47.github.io/sicegar/
NeedsCompilation: no
Citation: sicegar citation info
Materials: README, NEWS
CRAN checks: sicegar results

Documentation:

Reference manual: sicegar.html , sicegar.pdf
Vignettes: Calculation of additional parameters of interest (source, R code)
Adjusting data to use with sicegar (source, R code)
Identifying the best-fitting model category (source, R code)
Fitting individual models (source, R code)
Allowing the lower asymptote parameter to vary freely (source, R code)
Introduction (source, R code)
Plotting the fitted models (source, R code)

Downloads:

Package source: sicegar_0.3.0.tar.gz
Windows binaries: r-devel: sicegar_0.2.4.zip, r-release: sicegar_0.2.4.zip, r-oldrel: sicegar_0.2.4.zip
macOS binaries: r-release (arm64): sicegar_0.2.4.tgz, r-oldrel (arm64): sicegar_0.2.4.tgz, r-release (x86_64): sicegar_0.2.4.tgz, r-oldrel (x86_64): sicegar_0.2.4.tgz
Old sources: sicegar archive

Linking:

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