Welcome to BEELINE’s documentation!

Overview of BEELINE

This site serves as the documentation for the code released under the Benchmarking gEnE reguLatory network Inference from siNgle-cEll transcriptomic data (BEELINE) project. The first part of this project is the BEELINE pipeline which provides tools to evaluate the performance of algorithms for the reconstruction of gene regulatory networks (GRNs) from single-cell RNAseq data. The second part of this project is BoolODE, a tool to automatically convert a Boolean model to an ODE model, and subsequently carry out stochastic simulations.

• BEELINE
  • Overview
  • Getting Started
  • Tutorial
    • Project outline
    • Input Datasets
    • Config files
    • Running the pipeline
    • Running the evaluation scripts
  • Details of supported algorithms
  • Developer Guide
    • Adding a new GRN inference method
    • Adding a new evaluation technique
  • API Reference
    • BLRun package
    • BLEval package
    • BLPlot package
• BoolODE
  • Overview
  • Tutorial
    • Defining an input model
    • Running BoolODE
    • Working with BoolODE output
  • Generating inputs for BEELINE
    • Compute Pseudotime using Slingshot
    • Generate dropouts from expression data
  • Command Line Options
  • API Reference
    • src package

Indices and tables

• Index
• Module Index
• Search Page