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
parallel_subtyping
Cell subtyping of h5mu file annotated with major types.
The input is expected to already carry a major cell-type annotation in
.obs (--obs_major_cell_type) on the modality to be subtyped (--modality).
Each major cell type is then subtyped independently, so that the annotation
is tailored to the cells within that group rather than the dataset as a
whole.
Nextflow
process_integrate_annotate
A pipeline to process, integrate and annotate single cell (multi-)omics data.
Available integration methods:
Harmony
scVI
Scanorama
BBKNN
Available annotation methods:
CellTypist
Harmony integration followed by KNN label transfer (harmony_knn)
scANVI (with scArches)
scVI integration followed by KNN label transfer (scvi_knn)
SingleR
When more than one annotation method is selected, a final consensus vote
combines the per-method predictions into a single consensus label.
Nextflow