Tutorial

Integration

before integration

../_images/pbmc_before_integration.png

after SCALEX integration

../_images/pbmc_integration.png

Projection

Map new data to the embeddings of reference

A pancreas reference was created by integrating eight batches.

Here, map pancreas_gse81547, pancreas_gse83139 and pancreas_gse114297 to the embeddings of pancreas reference.

../_images/pancreas_projection.png

Label transfer

Annotate cells in new data through label transfer

Label transfer tabula muris data and mouse kidney data from mouse atlas reference

mouse atlas reference

../_images/mouse_atlas_reference.png

query tabula muris aging and query mouse kidney

../_images/query_tabula_muris_aging.png ../_images/query_kidney.png

Integration scATAC-seq data

../_images/scATAC_integration.png

Integration cross-modality data

Integrate scRNA-seq and scATAC-seq dataset

../_images/cross-modality_integration.png

Spatial data (To be updated)

Integrating spatial data with scRNA-seq

Examples