Package: sicegar
Type: Package
Title: Analysis of Single-Cell Viral Growth Curves
Version: 0.3.0
Authors@R: c( 
    person(
      given = "Johanna",
      family = "Hardin",
      role = c("aut", "cre"),
      email = "jo.hardin@pomona.edu",
      comment = c(ORCID = "0000-0001-6251-1955")
    ),
    person(
      given = "Samuel",
      family = "Butler",
      role = c("aut"),
      email = "swbe2022@mymail.pomona.edu"
    ),
    person(
      given = "Phineus",
      family = "Choi",
      role = c("aut"),
      email = "pchm2023@mymail.pomona.edu"
    ),
    person(
      given = "Thomas",
      family = "Matheis",
      role = c("aut"),
      email = "tomp2024@mymail.pomona.edu"
    ),
    person(
      given = "Mira",
      family = "Terdiman",
      role = c("aut"),
      email = "mterdiman@berkeley.edu"
    ),
    person(
      given = "M. Umut",
      family = "Caglar",
      role = c("aut"),
      email = "umut.caglar@gmail.com"
    ),
    person(
      given = "Claus O.",
      family = "Wilke",
      role = c("aut"),
      email = "wilke@austin.utexas.edu",
      comment = c(ORCID = "0000-0002-7470-9261")
    )
  )  
Description: 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".
URL: https://github.com/wilkelab/sicegar/,
        https://hardin47.github.io/sicegar/
Imports: minpack.lm, fBasics, ggplot2, stats, dplyr
License: GPL-2 | GPL-3
Suggests: covr, cowplot, testthat, knitr, rmarkdown
VignetteBuilder: knitr
BugReports: https://github.com/hardin47/sicegar/issues
Collate: 'globals.R' 'categorize.R' 'categorize_h0.R' 'mainFunctions.R'
        'multipleFitFunction.R' 'multipleFitFunction_h0.R'
        'sigmoidalFitFunctions.R' 'sigmoidalFitFunctions_h0.R'
        'doublesigmoidalFitFunctions.R'
        'doublesigmoidalFitFunctions_h0.R' 'normalizationFunction.R'
        'sicegar.R' 'dataInputCheck.R' 'parameterCalculation.R'
        'parameterCalculation_h0.R' 'figureGeneration.R'
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Encoding: UTF-8
Repository: https://hardin47.r-universe.dev
Date/Publication: 2026-02-02 03:32:41 UTC
RemoteUrl: https://github.com/hardin47/sicegar
RemoteRef: HEAD
RemoteSha: 4205fbe3998871dd74b08ff4565e5a79b71c6006
NeedsCompilation: no
Packaged: 2026-07-02 09:06:44 UTC; root
Author: Johanna Hardin [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-6251-1955>),
  Samuel Butler [aut],
  Phineus Choi [aut],
  Thomas Matheis [aut],
  Mira Terdiman [aut],
  M. Umut Caglar [aut],
  Claus O. Wilke [aut] (ORCID: <https://orcid.org/0000-0002-7470-9261>)
Maintainer: Johanna Hardin <jo.hardin@pomona.edu>