lamindb.core.datasets.schmidt22_perturbseq

lamindb.core.datasets.schmidt22_perturbseq(basedir='.')

Perturb-seq collection of Schmidt22.

Subsampled and converted to h5ad from R file: https://zenodo.org/record/5784651

To reproduce the subsample: >>> adata = sc.read(‘HuTcellsCRISPRaPerturbSeq_Re-stimulated.h5ad’) >>> adata.obs = adata.obs[[‘cluster_name’]] >>> del adata.obsp >>> del adata.var[‘features’] >>> del adata.obsm[‘X_pca’] >>> del adata.uns >>> del adata.raw >>> del adata.varm >>> adata.obs = adata.obs.reset_index() >>> del adata.obs[‘index’] >>> sc.pp.subsample(adata, 0.03) >>> adata.write(‘schmidt22_perturbseq.h5ad’)

Return type:

Path