deli-chem 0.2.1

DNA encoded library sequence analysis software with custom library design support

DELi

DELi (DNA-Encoded Library informatics) is a Python library for working with DELs. It incorporates the whole pipeline post base-calling/sequencing including:

1. Barcode/DEL ID calling and cube file generation
2. Enumeration of chemical structures from building blocks
3. Disython and Monosynthon analysis
4. Generation of machine learning datasets and baseline models from DEL data
5. Various digestible reports to understand the DEL results

You can read the detailed documentation here.

Installing DELi

You can install DELi using pip on Python 3.13 or newer:

pip install deli-chem

Optional graph neural network (GNN) analysis dependencies:

pip install 'deli-chem[ml]'

Getting Started

You 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.

Why not a compiled language

DELi is written in Python for two reasons:

1. We wrote the first versions of it in Python
2. 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 uses uv for builds and dependency management. After cloning the repo, install with pip install -e . or uv sync.

Citation

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