Guides
Task-focused sections grouped by pipeline stage.
Preprocessing
Prepare AnnData
Downsample cells and build the embedding.
Content coming soon.
Feature selection
Select variable genes.
Content coming soon.
Finding loops
Find loops
Detect loops and test them on bootstrap samples.
Content coming soon.
Bootstrap settings
Sample count, sampling method, presence test.
Content coming soon.
Analyzing loops
Trajectories and gene trends
Fit paths around a loop and smooth gene expression along them.
Content coming soon.
Hodge decomposition
Embed loop edges with the Hodge Laplacian.
Content coming soon.
Plotting
Persistence diagrams, loop landscapes, loop rank.
Content coming soon.
Matching and I/O
Match loops
Match loops between datasets.
Content coming soon.
Save and load
Write and read scloop results with h5ad.
Content coming soon.