Logo
latest

Introduction:

  • Introduction

Getting started

  • Installation
  • Tutorial 1: Data handling
  • Tutorial 2: Pixel map integration
  • Tutorial 3: Scanpy and AnnData integration
  • Tutorial 4: Exploratory analysis
  • Tutorial 5: Statistical modeling

User guide:

  • The SpatialData object:
  • The PixelMap object
  • The SpatialStatistics object
  • Next Neighbor analysis and spatial contexts:
  • Integrating scanpy/Anndata

Modules:

  • plankton
    • plankton package
plankton.py
  • plankton
  • Edit on GitHub

plankton

  • plankton package
    • Submodules
    • plankton.graph module
      • SpatialGraph
        • SpatialGraph.distances
        • SpatialGraph.knn_entropy()
        • SpatialGraph.map_and_umap()
        • SpatialGraph.neighbor_types
        • SpatialGraph.neighbors
        • SpatialGraph.plot_entropy()
        • SpatialGraph.plot_umap()
        • SpatialGraph.run_umap()
        • SpatialGraph.umap
        • SpatialGraph.umap_0
        • SpatialGraph.umap_1
        • SpatialGraph.umap_js()
        • SpatialGraph.update_knn()
    • plankton.pixelmaps module
    • plankton.plankton module
    • plankton.stats module
      • co_cooccurrence()
      • co_occurrence()
      • get_histograms()
      • mor_normalize()
      • ripleys_k()
    • plankton.utils module
    • Module contents
Previous Next

© Copyright 2022, Sebastian Tiesmeyer. Revision 3c840eac.

Built with Sphinx using a theme provided by Read the Docs.