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:

10x PBMCs Atlas (pbmcs_10x_reference.rds)

Pancreatic Islet Cells Atlas (pancreas_plate-based_reference.rds)

Fetal Liver Hematopoiesis Atlas (fetal_liver_reference_3p.rds)

Healthy Fetal Kidney Atlas (kidney_healthy_fetal_reference.rds)

T cell CITE-seq atlas (tbru_ref.rds)

Cross-tissue Fibroblast Atlas (see here)

Cross-tissue Inflammatory Immune Atlas (zhang_reference.rds)

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.