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pyvia documentation
pyvia documentation

General

  • StaVia - Multi-Omic Single-Cell Cartography for Spatial and Temporal Atlases
  • Installation
  • Release History
  • StaVia Tutorial Videos
  • Parameters and Attributes
  • API
    • pyVIA core
    • Plotting
      • pyVIA.plotting_via.animate_atlas
      • pyVIA.plotting_via.animate_streamplot
      • pyVIA.plotting_via.get_gene_expression
      • pyVIA.plotting_via.plot_atlas_view
      • pyVIA.plotting_via.plot_differentiation_flow
      • pyVIA.plotting_via.plot_gene_trend_heatmaps
      • pyVIA.plotting_via.plot_piechart_viagraph
      • pyVIA.plotting_via.plot_population_composition
      • pyVIA.plotting_via.plot_sc_lineage_probability
      • pyVIA.plotting_via.plot_scatter
      • pyVIA.plotting_via.plot_trajectory_curves
      • pyVIA.plotting_via.plot_viagraph
      • pyVIA.plotting_via.via_streamplot
    • Util Functions for plotting
      • pyVIA.plotting_via.make_edgebundle_milestone
      • pyVIA.plotting_via.via_atlas_emb
      • pyVIA.plotting_via.via_forcelayout
      • pyVIA.plotting_via.via_mds
    • Datasets
      • VIA.datasets_via.cell_cycle
      • VIA.datasets_via.cell_cycle_cyto_data
      • VIA.datasets_via.embryoid_body
      • VIA.datasets_via.scATAC_hematopoiesis
      • VIA.datasets_via.scRNA_hematopoiesis
      • VIA.datasets_via.toy_disconnected
      • VIA.datasets_via.toy_multifurcating
  • Examples for installation checking

StaVia Atlas View Gallery

  • StaVia Atlas views
  • Large Mouse Embryo to Pup Developmental Atlas
  • StaVia Atlas Animations

StaVia for time-series

  • 1. Via 2.0 Cartography on Mouse Gastrulation
  • 2. Via 2.0 Cartography on Zebrahub (Trajectory Inference)
  • 3. Via 2.0 Cartography on Zebrahub (Visualization)

StaVia for spatial-temporal

  • Stavia Spatially aware cartography on MERFISH
  • StaVia TI for Spatio-temporal Analysis of single cell data

scRNA, velocity and scATAC seq Tutorials

  • scRNA-seq Human Hematopoiesis
  • Pancreas using RNA-velocity
  • Hemato using RNA-velocity
  • StaVia for scATAC-seq Hematopoiesis

Cytometry

  • Imaging cytometry Cell Cycle
  • 5. Using time-series metadata (mESC Cytof)

Basic Tutorials for Toy Data

  • 1. Basic workflow
  • 2. Disconnected Trajectories
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