Package: cellmig
Type: Package
Title: Uncertainty-aware quantitative analysis of high-throughput live
        cell migration data
Version: 1.0.0
Authors@R: c(
    person("Simo", "Kitanovski", email = "simokitanovski@gmail.com", 
    role = c("aut", "cre"), comment=c(ORCID="0000-0003-2909-5376")))
Description: High-throughput cell imaging facilitates the analysis of
        cell migration across many wells treated under different
        biological conditions. These workflows generate considerable
        technical noise and biological variability, and therefore
        technical and biological replicates are necessary, leading to
        large, hierarchically structured datasets, i.e., cells are
        nested within technical replicates that are nested within
        biological replicates. Current statistical analyses of such
        data usually ignore the hierarchical structure of the data and
        fail to explicitly quantify uncertainty arising from technical
        or biological variability. To address this gap, we present
        cellmig, an R package implementing Bayesian hierarchical models
        for migration analysis. cellmig quantifies condition- specific
        velocity changes (e.g., drug effects) while modeling nested
        data structures and technical artifacts. It further enables
        synthetic data generation for experimental design optimization.
License: GPL-3 + file LICENSE
Depends: R (>= 4.4.0)
Imports: base, ggplot2, ggforce, ggtree, patchwork, ape, methods, Rcpp
        (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>=
        2.18.1), rstantools (>= 2.4.0), stats, utils, scales
Suggests: BiocStyle, knitr, testthat
Encoding: UTF-8
NeedsCompilation: yes
biocViews: SingleCell, CellBiology, Bayesian, ExperimentalDesign,
        Software, BatchEffect, Regression, Clustering
BugReports: https://github.com/snaketron/cellmig/issues
URL: https://github.com/snaketron/cellmig
RoxygenNote: 7.3.1
VignetteBuilder: knitr
Biarch: true
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0),
        RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>=
        2.18.0)
SystemRequirements: GNU make
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        make libicu-dev libpng-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:37:29 UTC
RemoteUrl: https://github.com/bioc/cellmig
RemoteRef: RELEASE_3_22
RemoteSha: e77030e81bfdb7facf72bbe44f04e105ec0fbca2
Packaged: 2025-11-11 13:37:43 UTC; root
Author: Simo Kitanovski [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2909-5376>)
Maintainer: Simo Kitanovski <simokitanovski@gmail.com>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-11 13:43:50 UTC; windows
Archs: x64
