spaTransfer: transfer learning for single-cell and spatial transcriptomics data using non-negative matrix factorization

This repository contains the processed data for the analyses associated with the manuscript “spaTransfer: transfer learning for single-cell and spatial transcriptomics data using non-negative matrix factorization”. 

Once unzipped, the processed-data folder contains the following folders:

• dlpfc:
  • One folder for each of the dlpfc samples used in the manuscript (6 total), containing:
    • *-raw-SPE.RDS: SpatialExperiment objects containing the pre-QC Xenium raw counts matrices for each sample
    • *-filt-SPE.RDS: SpatialExperiment objects containing the post-QC Xenium counts matrices for each sample
    • *-filt-predLabels-SPE-bayesspace-logcounts.RDS: SpatialExperiment objects containing the post-QC Xenium counts matrices with spaTransfer domain predictions stored in the colData.
  • traam-outputs, a folder containing the spaTransfer outputs for the analyses in Figure 2.
  • 04_methodComparisons:
    • unsupervised_xenium_comparisons: 
      • One folder for each of the 5 unsupervised clustering methods benchmarked in Figure 4b. Each folder contains either SpatialExperiment or AnnData objects with the clustering method’s labels stored in the colData. 
      • *_labels.csv and *_metrics.csv: Labels and internal metrics for each of the clustering methods, respectively.
    • visium_comparisons:
      • One folder for each of the 3 label transfer methods benchmarked in Figure 4a. Eaach folder contains SpatialExperiment objects with the label transfer method’s labels stored in the colData.
      • *ARI*.csv: files contain ARI and NMI values for the label transfer methods.
• hpc:
  • One folder for each of the hpc samples used in the manuscript (6 total), containing:
    • *-raw-SPE.RDS: SpatialExperiment objects containing the pre-QC Xenium raw counts matrices for each sample
    • *-filt-SPE.RDS: SpatialExperiment objects containing the post-QC Xenium counts matrices for each sample
    • *-filt-predLabels-SPE-bayesspace-logcounts.RDS: SpatialExperiment objects containing the post-QC Xenium counts matrices with spaTransfer domain predictions stored in the colData.
  • traam-outputs, a folder containing the spaTransfer outputs for the analyses in Figure 3.
  • custom-panel-pseudobulkedByDomain-SPE.RDS: pseudobulked SpatialExperiment object used Figure S14-S16.