DGrowthR: A comprehensive workflow for growth curve analysis

This repository hosts the DGrowthR R package and the workflow for the detailed analysis of publicly available datasets mentioned in our pre-print. This workflow is designed to showcase the application of the DGrowthR package to model complex, non-linear dynamics of bacterial growth using Gaussian Process Regression.

Tip

For more details, check out our pre-print Statistical end-to-end analysis of large-scale microbial growth data with DGrowthR on bioRxiv.

DGrowthR is also available as a standalone Desktop-App for Windows and Apple (https://zenodo.org/records/15118187).

Installation Guide

To install the DGrowthR R package directly from this repository. First make sure you clone the repository and enter into the cloned folder. Then you can execute the following commands in R.

1. Ensure that you have the devtools package installed. If not, you can install it using the following command

# Install devtools
install.packages("devtools")

# Load the library
library(devtools)

2. Use the install function to install the DGrowthR package:

install()

Additionally, you must install the permApprox package in order to obtain gamma-approximated p-values.

remotes::install_github("stefpeschel/permApprox")

How to use DGrowthR.

An overview of the main functionalities of DGrowthR with concrete examples can be found in our tutorial vignette

Analysis workflow.

Additionally, you see our analysis of publicly available datasets from the Brochado 2018 and Brenzinger 2024 studies.

All steps are in our workflow folder

DGrowthR Overview