scRNA-seq

Here, you’ll learn how to manage a growing number of scRNA-seq datasets as a single queryable collection:

1. create a dataset (an Artifact) and seed a Collection ()

2. append a new dataset to the collection ()

3. query & analyze individual datasets ()

4. load the collection into memory ()

5. iterate over the collection to train an ML model ()

6. concatenate the collection to a single tiledbsoma array store ()

If you’re only interested in using a large curated scRNA-seq collection, see the CELLxGENE guide.

# pip install 'lamindb[jupyter,bionty]'
!lamin init --storage ./test-scrna --schema bionty

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→ initialized lamindb: testuser1/test-scrna

import lamindb as ln
import bionty as bt

ln.track("Nv48yAceNSh80003")  # <-- passing a uid is optional

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→ connected lamindb: testuser1/test-scrna

→ created Transform('Nv48yAceNSh80003'), started new Run('CiYtMJRb...') at 2025-03-10 13:25:35 UTC

→ notebook imports: bionty==1.1.2 lamindb==1.2.0

Populate metadata registries based on an artifact

Let us look at the standardized data of Conde et al., Science (2022), available from CELLxGENE. anndata_human_immune_cells() loads a subsampled version:

adata = ln.core.datasets.anndata_human_immune_cells()
adata

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AnnData object with n_obs × n_vars = 1648 × 36503
    obs: 'donor', 'tissue', 'cell_type', 'assay'
    var: 'feature_is_filtered', 'feature_reference', 'feature_biotype'
    uns: 'default_embedding'
    obsm: 'X_umap'

Let’s curate this artifact:

curator = ln.Curator.from_anndata(
    adata,
    var_index=bt.Gene.ensembl_gene_id,
    categoricals={
        adata.obs.donor.name: ln.ULabel.name,
        adata.obs.tissue.name: bt.Tissue.name,
        adata.obs.cell_type.name: bt.CellType.name,
        adata.obs.assay.name: bt.ExperimentalFactor.name,
    },
    organism="human",
)

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✓ added 4 records with Feature.name for "columns": 'donor', 'tissue', 'cell_type', 'assay'

# this runs a while, because this instance is still empty
curator.validate()

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• saving validated records of 'var_index'

✓ added 36283 records from public with Gene.ensembl_gene_id for "var_index": 'ENSG00000243485', 'ENSG00000237613', 'ENSG00000186092', 'ENSG00000238009', 'ENSG00000239945', 'ENSG00000239906', 'ENSG00000241860', 'ENSG00000241599', 'ENSG00000286448', 'ENSG00000236601', 'ENSG00000284733', 'ENSG00000235146', 'ENSG00000284662', 'ENSG00000229905', 'ENSG00000237491', 'ENSG00000177757', 'ENSG00000228794', 'ENSG00000225880', 'ENSG00000230368', 'ENSG00000272438', ...

• mapping "var_index" on Gene.ensembl_gene_id

!   220 terms are not validated: 'ENSG00000230699', 'ENSG00000241180', 'ENSG00000226849', 'ENSG00000272482', 'ENSG00000264443', 'ENSG00000242396', 'ENSG00000237352', 'ENSG00000269933', 'ENSG00000286863', 'ENSG00000285808', 'ENSG00000261737', 'ENSG00000230427', 'ENSG00000226822', 'ENSG00000273373', 'ENSG00000259834', 'ENSG00000224167', 'ENSG00000256374', 'ENSG00000234283', 'ENSG00000263464', 'ENSG00000203812', ...
    → fix typos, remove non-existent values, or save terms via .add_new_from_var_index()

• saving validated records of 'tissue'

✓ added 17 records from public with Tissue.name for "tissue": 'transverse colon', 'mesenteric lymph node', 'liver', 'skeletal muscle tissue', 'blood', 'spleen', 'lamina propria', 'ileum', 'caecum', 'thoracic lymph node', 'bone marrow', 'jejunal epithelium', 'thymus', 'omentum', 'duodenum', 'sigmoid colon', 'lung'

• saving validated records of 'cell_type'

✓ added 31 records from public with CellType.name for "cell_type": 'progenitor cell', 'megakaryocyte', 'effector memory CD4-positive, alpha-beta T cell', 'group 3 innate lymphoid cell', 'memory B cell', 'naive thymus-derived CD8-positive, alpha-beta T cell', 'plasmablast', 'classical monocyte', 'CD16-negative, CD56-bright natural killer cell, human', 'lymphocyte', 'alpha-beta T cell', 'naive B cell', 'effector memory CD8-positive, alpha-beta T cell, terminally differentiated', 'gamma-delta T cell', 'T follicular helper cell', 'CD8-positive, alpha-beta memory T cell', 'CD16-positive, CD56-dim natural killer cell, human', 'conventional dendritic cell', 'alveolar macrophage', 'dendritic cell, human', ...

• saving validated records of 'assay'

✓ added 3 records from public with ExperimentalFactor.name for "assay": '10x 5' v2', '10x 5' v1', '10x 3' v3'

• mapping "donor" on ULabel.name

!   12 terms are not validated: 'D496', '621B', 'A29', 'A36', 'A35', '637C', 'A52', 'A37', 'D503', '640C', 'A31', '582C'
    → fix typos, remove non-existent values, or save terms via .add_new_from("donor")

✓ "tissue" is validated against Tissue.name

• mapping "cell_type" on CellType.name

!   1 term is not validated: 'animal cell'
    → fix typos, remove non-existent values, or save terms via .add_new_from("cell_type")

✓ "assay" is validated against ExperimentalFactor.name

False

curator.add_new_from_var_index()

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✓ added 220 records with Gene.ensembl_gene_id for "var_index": 'ENSG00000230699', 'ENSG00000241180', 'ENSG00000226849', 'ENSG00000272482', 'ENSG00000264443', 'ENSG00000242396', 'ENSG00000237352', 'ENSG00000269933', 'ENSG00000286863', 'ENSG00000285808', 'ENSG00000261737', 'ENSG00000230427', 'ENSG00000226822', 'ENSG00000273373', 'ENSG00000259834', 'ENSG00000224167', 'ENSG00000256374', 'ENSG00000234283', 'ENSG00000263464', 'ENSG00000203812', ...

curator.add_new_from("donor")
curator.add_new_from("cell_type")

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✓ added 12 records with ULabel.name for "donor": 'A52', '640C', 'A29', 'A37', '582C', '621B', 'A31', '637C', 'A36', 'D496', 'D503', 'A35'

✓ added 1 record with CellType.name for "cell_type": 'animal cell'

curator.validate()

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✓ "var_index" is validated against Gene.ensembl_gene_id

✓ "donor" is validated against ULabel.name

✓ "tissue" is validated against Tissue.name

✓ "cell_type" is validated against CellType.name

✓ "assay" is validated against ExperimentalFactor.name

True

When we create a Artifact object from an AnnData, we automatically curate it with validated features and labels:

artifact = curator.save_artifact(key="datasets/conde22.h5ad")

It is annotated with rich metadata:

artifact.describe()

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Artifact .h5ad/AnnData
├── General
│   ├── .uid = 'gPsOLFy0DnkG6iH00000'
│   ├── .key = 'datasets/conde22.h5ad'
│   ├── .size = 57612943
│   ├── .hash = 't_YJQpYrAyAGhs7Ir68zKj'
│   ├── .n_observations = 1648
│   ├── .path = /home/runner/work/lamin-usecases/lamin-usecases/docs/test-scrna/.lamindb/gPsOLFy0DnkG6iH00000.h5ad
│   ├── .created_by = testuser1 (Test User1)
│   ├── .created_at = 2025-03-10 13:26:22
│   └── .transform = 'scRNA-seq'
├── Dataset features/.feature_sets
│   ├── var • 36503                 [bionty.Gene]                                                       
│   │   MIR1302-2HG                 float                                                               
│   │   FAM138A                     float                                                               
│   │   OR4F5                       float                                                               
│   │   OR4F29                      float                                                               
│   │   OR4F16                      float                                                               
│   │   LINC01409                   float                                                               
│   │   FAM87B                      float                                                               
│   │   LINC01128                   float                                                               
│   │   LINC00115                   float                                                               
│   │   FAM41C                      float                                                               
│   └── obs • 4                     [Feature]                                                           
│       assay                       cat[bionty.ExperimentalF…  10x 3' v3, 10x 5' v1, 10x 5' v2          
│       cell_type                   cat[bionty.CellType]       CD16-negative, CD56-bright natural kille…
│       donor                       cat[ULabel]                582C, 621B, 637C, 640C, A29, A31, A35, A…
│       tissue                      cat[bionty.Tissue]         blood, bone marrow, caecum, duodenum, il…
└── Labels
    └── .tissues                    bionty.Tissue              transverse colon, mesenteric lymph node,…
        .cell_types                 bionty.CellType            progenitor cell, megakaryocyte, effector…
        .experimental_factors       bionty.ExperimentalFactor  10x 5' v2, 10x 5' v1, 10x 3' v3          
        .ulabels                    ULabel                     A52, 640C, A29, A37, 582C, 621B, A31, 63…

Seed a collection

Let’s create a first version of a collection that will encompass many h5ad files when more data is ingested.

Note

To see the result of the incremental growth, take a look at the CELLxGENE Census guide for an instance with ~1k h5ads and ~50 million cells.

collection = ln.Collection(artifact, key="My versioned scRNA-seq collection").save()

For this version 1 of the collection, collection and artifact match each other. But they’re independently tracked and queryable through their registries:

collection.describe()

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Collection 
└── General
    ├── .uid = 'M5hB1OJJaQESfJCE0000'
    ├── .key = 'My versioned scRNA-seq collection'
    ├── .hash = 'DuyXxlMxwF92YehyBLbhKg'
    ├── .created_by = testuser1 (Test User1)
    ├── .created_at = 2025-03-10 13:26:25
    └── .transform = 'scRNA-seq'

Access the underlying artifacts like so:

collection.artifacts.df()

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	uid	key	description	suffix	kind	otype	size	hash	n_files	n_observations	_hash_type	_key_is_virtual	_overwrite_versions	space_id	storage_id	schema_id	version	is_latest	run_id	created_at	created_by_id	_aux	_branch_code
id
1	gPsOLFy0DnkG6iH00000	datasets/conde22.h5ad	None	.h5ad	dataset	AnnData	57612943	t_YJQpYrAyAGhs7Ir68zKj	None	1648	sha1-fl	True	False	1	1	None	None	True	1	2025-03-10 13:26:22.730000+00:00	1	None	1

See data lineage:

collection.view_lineage()