MetPhenoR

The complete workflow including examples can be found in vignettes/MetPhenoR.html. A flowchart of the package can be found in man/figures/MetPhenoR_workflow_flowchart.png

Installation

MetPhenoR is available on CRAN:

install.packages("MetPhenoR")

Installation from GitHub

Install the latest version directly from GitHub remotes package:

# Install remotes if you haven't already
if (!require("remotes", quietly = TRUE)) {
  install.packages("remotes")
}

# Install MetPhenoR from GitHub
remotes::install_github(KatjaDanielzik/MetPhenoR)

Data Preparation

Before analyzing your data:

Create a new folder (e.g., Analysis).
Copy all your RawRead.csv and PlateInfo.csv files into this folder.
In PlateInfo.csv, create or select one column (e.g., Sample) to store experimental metadata.
Format entries like:
cell.line_variable1_variable_2
H460_treatment_2h
→ Use underscores, no spaces, and consistent capitalization (R is case-sensitive!).

Never use spaces — this causes errors in read_folder().

Key Features

Feature	Function
Noise correction: `OD(590nm) - OD(740nm)`	Removes background noise (valid for adherent cells only).
`qc_data()` plot	Spot missing files, inconsistent conditions, or technical issues early.
`classify_growth_curve_types()`	Identify flat, dropping, or noisy curves.
AUC + normalization	Compare across plates and conditions.
Built-in annotations	KEGG pathways (PM-M01/M02), drug info (PM-M11–M14).
Heatmaps & violin plots	Visualize biological trends.

Important Limitations

Not for bacteria or suspension cultures: OD(740nm) reflects cell growth in these systems.
AUC does not capture curve shape: two very different curves can have the same AUC.
Does not account for cell growth: if your cells grow rapidly, this may confound results.
Does not interpret biological meaning: a “hit” in a pathway does not imply activation.

Troubleshooting

Issue	Solution
`No data in qc_data()`	Check for spaces and variable names `Sample` column; ensure all files are in the folder.
`Filtering didn’t work`	Double-check `plate_type` and `filters` spelling.
`Plot is blank`	Check if `processed_data` contains data after filtering.

Contact

Have questions, feedback, or want to contribute?
Open an Issue