microdiluteR

A framework for analyzing broth microdilution assays from 96-well plate designs.

https://github.com/silvia-eckert/microdiluter

Repository

A framework for analyzing broth microdilution assays from 96-well plate designs.

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  warning = FALSE,
  message = FALSE,
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/",
  out.width = "100%"
)
```

# microdiluteR 
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## :notebook: Background

The `microdiluteR` package is designed to help researchers tidy up data from photometer plates and provides functions to easily add metadata, regardless of whether the user is processing a single plate or multiple plates with complex metadata structures. This package was developed with a special focus on the analysis of [broth microdilution assays](https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/broth-dilution). A detailed tutorial can be found [here](https://silvia-eckert.github.io/microdiluteR/).

## :pushpin: Citation
Creating this package was a lot of work, and I made it available for free. If you use this package for your publication, be fair and cite it, e.g. using the following `biblatex`  entry:

```{r citation, eval = FALSE}
@software(eckert_micodiluteR_2024,
  author  = {Eckert, Silvia},
  title   = {microdiluteR},
  version = {1.0.1.},
  date    = {2024-05-13}
  year    = {2024},
  note    = {R package version 1.0.1, available from CRAN},
  url     = {https://cran.r-project.org/package=microdiluteR}
  doi     = {10.5281/zenodo.11186926}
)
```

Or you can cite as follows using the [APA](https://en.wikipedia.org/wiki/APA_style) citation style:

```{r apa, eval = FALSE}
Eckert, S. (2024). microdiluteR (Version 1.0.1) [Software]. DOI: 10.5281/zenodo.11186926. Retrieved from: https://CRAN.R-project.org/package=microdiluteR
```

Or use `citation("microdiluteR")` to retrieve citation information after installing the R package.

## :floppy_disk: Installation

You can install the CRAN version of `microdiluteR` with:

```{r cran_installation, eval = FALSE}
install.packages("microdiluteR")
```
You can install the development version of `microdiluteR` from GitHub with:

```{r github_installation, eval = FALSE}
# install.packages("devtools") # if not installed already
devtools::install_github("silvia-eckert/microdiluteR")
```

## :joystick: Usage

You can load `microdiluteR` as follows:

```{r library}
library(microdiluteR)
```

Let's try out the main function `tidy_plates()` with example data:
```{r data}
data(bma)
bma[1] # file name is bma_grp1_exp2_T0
```

For the example data, the corresponding metadata is stored as an attribute:
```{r attribute}
attr(bma, "metadata")
```

Let's add the metadata and create a tidy data frame for further processing:
```{r function}
tidy_data <- tidy_plates(bma[1],
                         how_many = "single",
                         direction = "horizontal",
                         validity_method = "threshold",
                         threshold = 0.355, # values above this are set as invalid
                         group_ID = "Group 1", # optional
                         experiment_name = "Experiment A", # optional
                         treatment_labels = rep(c("10%", "30%", "100%", "Control"), each = 2),
                         concentration_levels = rep(c(100,200), times = 4))

# Let's rename some columns for convenience
names(tidy_data)[names(tidy_data) == 'Position'] <- 'Pos'
names(tidy_data)[names(tidy_data) == 'Value'] <- 'Val'
names(tidy_data)[names(tidy_data) == 'Treatment'] <- 'Treat'
names(tidy_data)[names(tidy_data) == 'Concentration'] <- 'Conc'
names(tidy_data)[names(tidy_data) == 'Timepoint'] <- 'TP'
```

This is the resulting table:
```{r result_table}
tidy_data
```

## :hammer_and_wrench: Issues
If you find a :beetle: in the code, feel free to write this in the
[Issues](https://github.com/silvia-eckert/microdiluteR/issues) section. If you want to contribute to this
package or suggest a new feature, feel free to use the
[Pull Requests](https://github.com/silvia-eckert/microdiluteR/issues) section.

## :scroll: License
This repository and the files therein are licensed under the [GPL-3.0 license](https://www.gnu.org/licenses/gpl-3.0.html.en).

---

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Owner

Citation (CITATION.cff)

cff-version: 1.0.1
message: "If you use this software, please cite it as below."
authors:
- family-names: "Eckert"
  given-names: "Silvia"
  orcid: "https://orcid.org/0000-0002-8896-1046"
title: "microdiluteR"
version: 1.0.1
doi: 10.5281/zenodo.11186926
date-released: 2024-05-13
url: "https://cran.r-project.org/package=microdiluteR"

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