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microdiluteR  

Analysis of Broth Microdilution Assays
View on CRAN: Click here


Download and install microdiluteR package within the R console
Install from CRAN:
install.packages("microdiluteR")

Install from Github:
library("remotes")
install_github("cran/microdiluteR")

Install by package version:
library("remotes")
install_version("microdiluteR", "1.0.1")



Attach the package and use:
library("microdiluteR")
Maintained by
Silvia Eckert
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2024-05-13
Latest Update: 2024-05-13
Description:
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>.
How to cite:
Silvia Eckert (2024). microdiluteR: Analysis of Broth Microdilution Assays. R package version 1.0.1, https://cran.r-project.org/web/packages/microdiluteR. Accessed 12 Nov. 2024.
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