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processed_data.md

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Processed Data

We provide preprocessed versions of public data sets used to evaluate scNym below. All datasets are formatted following the AnnData conventions.

Human

  1. hPBMS Stimulated/Control -- We used the authors' annotations in the .obs["cell"] attribute. We split experimental conditions based on the authors annotations in the .obs["stim"] attribute. We obtained source data from GEO at accession GSE96583.

Mouse

  1. Tabula Muris 10x -- We used the authors' annotations in the .obs["cell_ontology_class"] attribute. We obtained source data from the authors' website.
  2. Tabula Muris Smart-seq2 -- We used the authors' annotations in the .obs["cell_ontology_class"] attribute. We obtained source data from the authors' website.
  3. Mouse Cell Atlas Lung data with manual annotations -- We added manual annotations in the .obs["cell_ontology_class"] attribute. We obtained source data from the authors' website.
  4. 10x Visium Spatial Transcriptomics of Mouse Brain Section 0 -- We added manual annotations in the .obs["cell_ontology_class"] attribute. We obtained source data from 10x Genomics.
  5. 10x Visium Spatial Transcriptomics of Mouse Brain Section 1 -- We added manual annotations in the .obs["cell_ontology_class"] attribute. We obtained source data from 10x Genomics.
  6. Cross-Technology comparison in the Mouse Cortex -- We used the authors' annotations in the "CellType" attribute. We obtained source data from the Broad Institute Single Cell Portal.
  7. Cross-Technology comparison in the Mouse Kidney -- We mapped the authors' annotations into the "cell ontology" namespace and stored these annotations in the "cell_ontology_class" attribute. We removed cells with ambiguous cell types under the cell ontology (2310 cells total). We identified unique experimental domains using the "Protocol" attribute. We obtained data from GEO at GSE141115.

Rat

  1. Rat Aging Cell Atlas -- We translated the authors' annotations into the "cell ontology class" namespace and stored these annotations in the .obs["cell_ontology_class"] attribute. We obtained source data from GEO at accession GSE137869.