DELi (DNA-Encoded Library informatics) is a Python library for working with DELs. It incorporates the whole pipeline post base-calling/sequencing including:
- Barcode/DEL ID calling and cube file generation
- Enumeration of chemical structures from building blocks
- Disython and Monosynthon analysis
- Generation of machine learning datasets and baseline models from DEL data
- Various digestible reports to understand the DEL results
You can read the detailed documentation here.
You can install DELi using pip for any OS/Machine that supports Python 3.10+:
pip install deli-chemYou can use DELi as a command line tool (see the docs for more details) or as a python package
import deli
print(deli.__version__)Note
installing DELi uses deli-chem but to use DELi after install make sure to use deli and that you have no other packages named deli
For an end-to-end workflow of running DELi with open source libraries and selections (Enumerate, Decode, Analyze), see the examples documentation.
DELi is written in Python for two reasons:
- We wrote the first versions of it in Python
- Python is the language most scientists in our field know, so it makes contributions from other DEL experts easier
It is true that DELi would be faster as a compiled C++ or Rust program, but we have optimized the DELi enough that runtime isn't much of an issue. We hope to someday write a Rust version of DELi (at least for decoding and enumeration) but those plans are not yet in motion.
Note for developers: DELi is built using poetry. You can use poetry build to build from source after
cloning the repo. Be on the lookout for contribution docs in the near future!
If you use DELi in your research, please cite our paper:
Wellnitz J, Novy B, Maxfield T, Lin S-H, Zhilinskaya I, Axtman M, Leisner T, Merten E, Norris-Drouin JL, Hardy BP, Pearce KH, Popov KI. (2025). Open-Source DNA-Encoded Library informatics Package for Design, Decoding, and Analysis: DELi. bioRxiv. https://doi.org/10.1101/2025.02.25.640184