DELi Documentation

Welcome to DELi’s documentation!

DELi is a Python library for working with DNA-encoded libraries (DELs). It requires Python 3.13 or newer.

You can install DELi using pip:

pip install deli-chem

Optional GNN analysis dependencies: pip install 'deli-chem[ml]'

End-to-end example workflows are in the examples directory.

Introduction

• DELi Glossary
  • Glossary
• DELi compound naming conventions

Configuration

• DELi Configuration
  • File Format
• DELi Data Directory
  • Creating a DELi Data Directory
  • How to use the Data Dir
  • Setting the DELi Data Directory
  • How to Best Use the Data Directory

Defining DELs

• Selection Files
  • Selection File Format
  • Sequenced Selection File Format
  • Decode Settings in the Selection File
• Defining DELs for use in DELi
  • Defining Libraries
  • Defining Building Blocks Sets
  • Defining Enumerators
  • Defining Reactions
  • Defining Tool Compounds
  • Defining Hamming Codes

Running DELi

• DELi Command Line Interface
• Parallelization in DELi
  • Running parallel decoding with Nextflow

Enumeration

• Enumeration
  • How Enumeration Works
  • Enumeration Python API
  • Enumeration with DELi
  • Enumerating to a file
  • Single Compound Enumeration
  • Command-Line Interface
  • Loading Enumerators from Files

Decoding

• DEL Decoding
  • Decoding Algorithm
  • Barcode Calling Hashmaps
  • Decoding Outcomes
  • Tool Compounds
  • Running DELi Decode
  • Decoding Settings

Analysis

• DELi Analysis Documentation
  • Overview
  • Automated Analysis Mode
  • Development and Testing Mode
  • Manual Analysis Mode
• Analysis configuration (YAML)
  • General section
  • Indexes and controls
  • Flags block
• Contributing to DELi Analysis

Development

• Testing and coverage
  • Generate a coverage report
  • Current coverage (DELi 0.2.1)
  • Interpreting these numbers
• Development FAQs

API Reference

• deli
  • Submodules

Indices and tables

• Index

• Module Index

• Search Page