Published July 9, 2021
| Version 1.1
Dataset
Restricted
Symphony pre-built single-cell reference atlases
Description
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.