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neckaR

License: MIT

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

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 with:

# 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:

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:

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:

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.

Why neckaR?

The 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.