Retip 2.0 was updated and released in June 2024 by oloBion.
Retip is a tool for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis, available as both a Python package and an R package. Retention time calculation can be useful in identifying unknowns and removing false positive annotations. The Python package uses four different machine learning algorithms to built a stable, accurate and fast RT prediction model:
- Random Forest: a decision tree algorithms.
- XGBoost: an extreme Gradient Boosting for tree algorithms.
- AutoGluon: is an automatic machine learning library.
- H2O AutoML: is an automatic machine learning tool.
Retip 2.0 requires Python 3.10 and it is recommended to use the Anaconda, miniconda or Mamba package managers to easily install and run the package.
Once Anaconda is installed, simply check out the Retip repository and create an environment named pyretip:
git clone https://github.com/oloBion/pyRetip.git
cd pyRetip
conda env createRun conda activate pyretip followed by jupyter lab. Then, open the notebooks folder to start working through code examples to learn how Retip works.
Run conda activate pyretip and install the curses dependency by running pip install windows-curses. Then, run jupyter lab and open the notebooks folder to start working through code examples to learn how Retip works.