Repository navigation
Convert: SCope looms from SCENIC+, pySCENIC and pycistopic #27
Description
Part of #20. Builds on the loom reader in #26.
These looms follow SCope conventions that a generic loom reader mangles (compound arrays, compressed JSON metadata).
Plan
Detection: loom with a MetaData global attribute and/or col_attrs/RegulonsAUC.
| SCope loom | AnnData |
|---|---|
global MetaData (base64-encoded, zlib-compressed JSON: embeddings, clusterings, annotations, regulon thresholds) |
decoded into uns/scope/… |
col_attrs/RegulonsAUC (compound array, cells × regulons) |
obsm["X_regulons_auc"], regulon names in uns/scope/regulons |
row_attrs/Regulons (binary compound array, genes × regulons) |
varm["regulons"] |
col_attrs/Embedding, Embeddings_X, Embeddings_Y |
obsm["X_<embedding name from MetaData>"] |
col_attrs/Clusterings |
categorical obs columns, labels taken from MetaData |
other SCope global attrs (SCopeTreeL1..3, Genome, CreationDate) |
uns/scope/… |
pycistopic looms (export_region_accessibility_to_loom, export_gene_activity_to_loom) store regions or gene activity in /matrix — detect region-style names (chr:start-end) and use them as var_names.
Export (stretch goal): h5ad → SCope loom with regulon AUC and embeddings, so results can be browsed in SCope.
Needs
Real pySCENIC, SCENIC+ and pycistopic looms to build small fixtures from.
- Source: the public SCope instance at https://scope.aertslab.org/#/6ac5a322-5e87-4a2c-b732-3ab5ef4cd21f/*/welcome hosts published SCope looms (pySCENIC, SCENIC+, pycistopic), which can be downloaded from the dataset view.
- Plan: download one loom of each flavour (gene-based pySCENIC, SCENIC+ eRegulon, pycistopic region accessibility / gene activity), record the dataset name and URL, and inspect the layout (
adata ls/h5ls -r). Then write a script undertests/fixtures/that cuts each one down to a few hundred cells and genes while keeping every attribute, compound array and theMetaDatastructure. Only the cut-down fixtures are committed. - Full-size files can back an optional test under the
integrationmarker that downloads them on demand.
Note
Current SCENIC+ writes MuData (.h5mu) rather than looms; that is tracked in #31.
Activity
adata convertto and from h5ad/zarr #20Claptar commentedon Oct 20, 2026
Done in #62, released in 0.12.0.
adata convertreads a SCope loom's regulons (obsm["RegulonsAUC"],varm["Regulons"], dataframes with the regulons' names as columns), embeddings (obsm["X_<name>"]) and clusterings (categorical obs columns) named fromMetaData, andMetaDataitself intouns["scope"]. It matches the pySCENIC tutorial's loompy recipe on Zenodo 10944066's pbmc3k loom, whichanndata.read_loomrefuses. Region-based looms (SCENIC+, pycistopic) are named by region. Export to SCope is #61.