Symphony pre-built single-cell reference atlases

Pre-built Symphony reference objects that can be downloaded and used to map new query datasets.

The Symphony algorithm is used to perform reference mapping to these atlases. 

• Preprint: https://www.biorxiv.org/content/10.1101/2020.11.18.389189v2
• Usage: https://github.com/immunogenomics/symphony

References available for download:

1. 10x PBMCs Atlas (pbmcs_10x_reference.rds)
2. Pancreatic Islet Cells Atlas (pancreas_plate-based_reference.rds)
3. Fetal Liver Hematopoiesis Atlas (fetal_liver_reference_3p.rds)
4. Healthy Fetal Kidney Atlas (kidney_healthy_fetal_reference.rds)
5. T cell CITE-seq atlas (tbru_ref.rds)
6. Cross-tissue Fibroblast Atlas (see here)
7. Cross-tissue Inflammatory Immune Atlas (here)
8. Tabula Muris Senis (FACS) Atlas (TMS_facs_reference.rds)

To read in a reference into R, one may simply execute: reference = readRDS('path/to/reference_name.rds')

Note: To be able to map query datasets into the reference UMAP coordinates, you must also download the corresponding 'uwot_model' file and set the reference$save_uwot_path.

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Updated 1/15/2026: It was brought to our attention that the Fibroblast Atlas link in previously published versions was no longer active. We have now reuploaded the Fibroblast Atlas .rds object.