Dataset Open Access

Symphony pre-built single-cell reference atlases

Kang, Joyce

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. 

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.

Files (2.1 GB)
Name Size
fetal_liver_reference_3p.rds
md5:042e72efc7ed52dfd50fe0090db15acd
107.5 MB Download
fetal_liver_uwot_model
md5:7e4afcc76c5a73ffd86b5f8fa7602d70
86.0 MB Download
kidney_healthy_fetal_reference.rds
md5:9001383dde6457d51435f67d4a959168
21.8 MB Download
kidney_healthy_fetal_uwot_model
md5:318a6274612457f45db899439b8927d9
21.1 MB Download
pancreas_plate-based_reference.rds
md5:e802bde77f5e06532b7621b071dbb40f
6.2 MB Download
pancreas_plate-based_uwot_model
md5:d1dd2e837a492d3423f5b37450b87fcc
5.1 MB Download
pbmcs_10x_reference.rds
md5:2d8a1087b7f550335d8030317384e532
21.4 MB Download
pbmcs_10x_uwot_model
md5:014b3df9ba0e370d635506cffffb9e7b
16.1 MB Download
tbru_ref.rds
md5:fcad41f191d1d0ee5626c39cdac1da07
557.0 MB Download
tbru_uwot_model
md5:62956757682f247939bc137accfb5e52
359.8 MB Download
TMS_facs_reference.rds
md5:04029ae37c587d605390b15aea0310ef
252.1 MB Download
TMS_facs_uwot_model
md5:8d5ef563b7077493a197322930406e8a
106.1 MB Download
zhang_reference.rds
md5:04dad4b00e752d315a64be4a111eefad
326.7 MB Download
zhang_uwot_model
md5:ae00afdc665c9b8b14d9f1e1df9e673f
215.5 MB Download
  • https://www.biorxiv.org/content/10.1101/2020.11.18.389189v2

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