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 
[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 |
Documentation:
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