move_anndata_slots
Move slots (.obs, .var, .obsm, .varm, .obsp, .varp, .uns) from a modality
in a source MuData file into a modality in a target MuData file.
The specified slots are copied from the source modality into the target
modality.
Python
parallel_annotation
Run multiple annotation methods from OpenPipeline in parallel on the same
preprocessed query h5mu input, then merge each method's predictions
(predicted labels and probabilities in .obs, and integrated embeddings in
.obsm for the integration-based methods) back into a single output h5mu.
These are label-projection (reference-based) methods: they transfer labels from
a labelled --reference onto the query (CellTypist can alternatively use a
pretrained --celltypist_model).
Nextflow
parallel_integration
Run multiple integration methods from OpenPipeline in parallel on the same
preprocessed h5mu input, then merge each method's annotations (leiden cluster
labels in .obs, integrated embeddings and UMAPs in .obsm, neighbor graphs in
.obsp and .uns) back into a single output h5mu.
Available integration methods: Harmony, scVI, Scanorama, BBKNN.
Nextflow