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Quick start tutorial:

  • Mapping human lymph node cell types to 10X Visium with Cell2location

Common errors, using containers:

  • Common errors
  • Using docker image
  • Using singularity image

API:

  • Initial gene filtering
  • Reference signatures (NB regression)
  • Reference signatures (hard-coded, cell type hierarchy)
  • Cell2location: spatial mapping (scvi-tools/pyro)
  • Downstream Analysis Models
  • Plotting
  • General utils
  • Pyro and scvi-tools infrastructure classes
  • Statistical distribution classes

Nanostring WTA Tutorial (pymc3):

  • Installation of pymc3 version with GPU support
  • Running cell2location on NanostringWTA data
cell2location
  • »
  • Python Module Index

Python Module Index

c
 
c
- cell2location
    cell2location.cluster_averages.cluster_averages
    cell2location.cluster_averages.markers_by_hierarhy
    cell2location.cluster_averages.select_features
    cell2location.distributions
    cell2location.models.base._pyro_mixin
    cell2location.models.base.base_model
    cell2location.models.downstream.ArchetypalAnalysis
    cell2location.models.downstream.CoLocatedGroupsSklearnNMF
    cell2location.plt
    cell2location.plt.mapping_video
    cell2location.plt.plot_expected_vs_obs
    cell2location.plt.plot_factor_spatial
    cell2location.plt.plot_heatmap
    cell2location.plt.RotateCrop
    cell2location.utils.filtering

© Copyright 2022, Vitalii Kleshchevnikov, Artem Shmatko, Emma Dann, Artem Lomakin, Alexander Aivazidis, Bayraktar Lab. Revision 47c8d6dc.

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