Welcome to PHLOWER’s documentation!

PHLOWER is a Python library for single cell trajectory inference using Hodge Laplacian Decomposition.

Getting started

• About PHLOWER
  • Incidence matrix
  • Hodge Laplacian
  • Trajectory sampling
  • Cumulative trajectory embedding and tree inference
  • References
• Installation
  • system dependences
  • install from pypi
  • install newest phlower version
  • Run
• Tutorial
  • Fibroblast to neuron
  • Kidney
  • Simulated data: Diffusion-limited aggregation Tree
  • Pancreas
  • Neurogenesis

API Reference

• API
  • tools: tl
  • external: ext
  • plotting: pl

datasets

• Datasets
  • Fibroblast to neuron
  • Kidney
  • Simulated data: Diffusion-limited aggregation Tree
  • Pancreas
  • Neurogenesis

downstream

• Regulators
  • Branch regulator detection
  • Main branches regulator detection