microdiluteR: Analysis of Broth Microdilution Assays

A framework for analyzing broth microdilution assays in various 96-well plate designs, visualizing results and providing descriptive and (simple) inferential statistics (i.e. summary statistics and sign test). The functions are designed to add metadata to 8 x 12 tables of absorption values, creating a tidy data frame. Users can choose between clean-up procedures via function parameters (which covers most cases) or user prompts (in cases with complex experimental designs). Users can also choose between two validation methods, i.e. exclusion of absorbance values above a certain threshold or manual exclusion of samples. A function for visual inspection of samples with their absorption values over time for certain group combinations helps with the decision. In addition, the package includes functions to subtract the background absorption (usually at time T0) and to calculate the growth performance compared to a baseline. Samples can be visually inspected with their absorption values displayed across time points for specific group combinations. Core functions of this package (i.e. background subtraction, sample validation and statistics) were inspired by the manual calculations that were applied in Tewes and Muller (2020) <doi:10.1038/s41598-020-67600-7>.

Version: 1.0.1
Depends: R (≥ 4.3)
Imports: dplyr (≥ 1.1.4), ggh4x (≥ 0.2.8), ggplot2 (≥ 3.5.0), ggthemes (≥ 5.0.1), magrittr (≥ 2.0.3), purrr (≥ 1.0.2), rlang (≥ 1.1.3), rstatix (≥ 0.7.2), stringr (≥ 1.5.1), tibble (≥ 3.2.1), tools (≥ 4.3.3), vctrs (≥ 0.6.5)
Suggests: knitr (≥ 1.4.6), rmarkdown (≥ 2.26), testthat (≥ 3.0.0)
Published: 2024-05-13
DOI: 10.32614/CRAN.package.microdiluteR
Author: Silvia Eckert ORCID iD [aut, cre]
Maintainer: Silvia Eckert <seckert-dev at posteo.de>
BugReports: https://github.com/silvia-eckert/microdiluteR/issues
License: GPL (≥ 3)
URL: https://silvia-eckert.github.io/microdiluteR/
NeedsCompilation: no
Materials: README
CRAN checks: microdiluteR results


Reference manual: microdiluteR.pdf


Package source: microdiluteR_1.0.1.tar.gz
Windows binaries: r-devel: microdiluteR_1.0.1.zip, r-release: microdiluteR_1.0.1.zip, r-oldrel: microdiluteR_1.0.1.zip
macOS binaries: r-release (arm64): microdiluteR_1.0.1.tgz, r-oldrel (arm64): microdiluteR_1.0.1.tgz, r-release (x86_64): microdiluteR_1.0.1.tgz, r-oldrel (x86_64): microdiluteR_1.0.1.tgz


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