README.md

Squidpy reproducibility

Code to reproduce the analysis and figures in the Squidpy manuscript (preprint on bioRxiv). For the main documentation, examples and tutorials, please visit the official Squidpy documentation.

Datasets

Code for preparing the datasets available in squidpy.datasets and used in the manuscript can be found in here

Main figures

• Figure 2
  • panels b-c
  • panels d-e
  • panels f-i
  • panels j-k
• Figure 3
  • panel a
  • panels b-e
  • panel f
• Figure 4
  • panels a-d,g-j
  • panels e,f

Supplementary figures

• Supplementary Figure 1
• Supplementary Figure 2
  • panels a-f
  • panel g
• Supplementary Figure 3
  • panel a
  • panel b
  • panels c-e
• Supplementary Figure 4
• Supplementary Figure 5
  • see tutorials for cellpose, stardist, and cellprofiler