growkar

SummarizedExperiment Infrastructure for Microbial Growth Phenotyping

Bioconductor version: 3.24 · Package version: 0.99.4

growkar provides Bioconductor-native infrastructure for high-throughput microbial growth phenotyping from plate-based assays such as optical density (OD) measurements. The package is built around SummarizedExperiment as its canonical data model, with OD measurements in assays, timepoint annotations in rowData, sample annotations in colData, and derived phenotypes in metadata. growkar supports data import, quality control, normalization, empirical growth-rate estimation, exponential-phase detection, and parametric modeling of growth dynamics. These workflows enable extraction of biologically meaningful phenotypes including lag time, growth rate, doubling time, and carrying capacity, and allow growth-derived phenotypes to be integrated with other Bioconductor analyses in microbial systems biology and multi-omics studies. The data-structure and analysis layers depend only on core Bioconductor infrastructure; graphing is optional and provided by 'plot_*' functions that are enabled when the suggested graphics package is installed.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("growkar")