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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# neckaR <a href='https://lisamaierlab.com/'><img src='man/figures/neckaR.png' align="right" height="139" /></a>
<!-- badges: start -->
[](https://github.com/jacodela/neckaR/blob/main/LICENSE.md)
<!-- badges: end -->
The `neckaR` package is a collection of functions for the analysis of bacterial
growth curves. The functions included in the package assist in the loading of files
with optical density readings and experimental design, the quality control of the
curves and the calculation of indices such as the area under the curve and the
maximum OD value. Created and used by the Maier Lab at the University of Tübingen,
Germany.
## Citation
If you use `neckaR`, please cite
> Müller P., de la Cuesta-Zuluaga J. et al.
High-Throughput Screening Strategies for the Identification of Active Compounds against Gut Bacteria. (2023).
The functions contained in `neckaR` are based on the code used in the paper:
> Maier, L., Pruteanu, M., Kuhn, M. et al.
Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555, 623–628 (2018).
[https://doi.org/10.1038/nature25979](https://doi.org/10.1038/nature25979)
# System Requirements
## Hardware requirements
The `neckaR` package requires only a standard personal computer with at least
8 GB RAM to support the in-memory operations.
## Software requirements
### OS Requirements
The package has been tested on the following operating systems:
* Windows 10
* macOS Ventura 13.3.1
* Linux Ubuntu 20.04
## Installation
You can install the development version of `neckaR` from [GitHub](https://github.com/) with:
```r
# install neckaR with the vignettes
install.packages("devtools")
devtools::install_github("Lisa-Maier-Lab/neckaR",
build_vignettes = TRUE,
force = TRUE)
```
A fresh installation of `neckaR` and its dependencies should take approximately 3 to 5 minutes, depending on the internet connection and the computer of the user.
### Dependencies
The `neckaR` package depends on the following libraries:
```
dplyr,
tidyr,
tibble,
stringr,
ggplot2,
purrr,
vctrs,
fitdistrplus,
readxl,
magrittr,
rlang,
grDevices,
stats,
data.table
```
These dependencies should be installed together with `neckaR`; if this is not the case, users can manually install them with the following command:
```r
install.packages(c("dplyr", "tidyr", "tibble", "stringr", "ggplot2", "purrr", "vctrs",
"fitdistrplus", "readxl", "magrittr", "rlang", "grDevices", "stats", "data.table"))
```
# Usage
You can check out the introductory vignette for a quick start tutorial by typing:
```r
vignette("Bacterial_Curve_Analysis", package="neckaR")
```
The execution of the complete vignette should take approximately 5 minutes, though
the functions within the `neckaR` package are thought to be executed interactively,
that it, the user is encouraged to verify the results of the intermediate steps and
to adjust the parameters of the steps accordingly.
For a comprehensive list of functions, you can explore the reference documentation:
```r
help(package="neckaR")
```
# Help & Contributing
`neckaR` is under active development, so user beware. Precisely because of that,
we rely you, the user, to point us towards things we can improve.
If you have questions or come across a bug, you can
[create a new issue here](https://github.com/jacodela/neckaR/issues).
# Why neckaR?
[The Neckar](https://en.wikipedia.org/wiki/Neckar) is a river that flows through
the state of Baden-Württemberg, in the southwest of Germany. On the banks of the
river Neckar lie the cities of Heidelberg and Tübingen, where this package has
been developed. First in the laboratory of Nassos Typas at EMBL and now in the
laboratory of Lisa Maier at the University of Tübingen. It is impossible not
to compare the meandering of the river with the bacterial growth curves. Although
to be perfectly honest, the word ends with an R and we had to take advantage of that.