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Robustness Tests for Tangram and CellTrek

Tangram

  1. Setup your environment using one of the .yml files
  2. Make a data folder and download the Tangram sample data by running:
# MOp 10Xv3 dataset
wget https://storage.googleapis.com/tommaso-brain-data/tangram_demo/mop_sn_tutorial.h5ad.gz -O data/mop_sn_tutorial.h5ad.gz
# SlideSeq data
wget https://storage.googleapis.com/tommaso-brain-data/tangram_demo/slideseq_MOp_1217.h5ad.gz -O data/slideseq_MOp_1217.h5ad.gz
wget https://storage.googleapis.com/tommaso-brain-data/tangram_demo/MOp_markers.csv -O data/MOp_markers.csv
gunzip -f data/mop_sn_tutorial.h5ad.gz
gunzip -f data/slideseq_MOp_1217.h5ad.gz
# Smart-Seq2_VISp_snRNAseq
wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115746/suppl/GSE115746_cells_exon_counts.csv.gz -O data/cells_exons_VISp.csv.gz
gunzip data/cells_exons_VISp.csv.gz
wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115746/suppl/GSE115746_complete_metadata_28706-cells.csv.gz -O data/metadata.csv.gz
gunzip data/metadata.csv.gz
  1. For STARMAP download https://zenodo.org/record/3967291#.Yz7aAexBxJU and transfer the Spatial/Starmap/visual_1020/20180505_BY3_1kgenes/ folder to data
  2. Convert the Smart-Seq2 and STARMAP datasets to h5ad files with convert_to_h5ad.py
  3. Run obtain_tangram_ad_maps to get all mappings
  4. Run obtain_tangram_expressions to get all gene expression predictions
  5. Run process_results to get the dataframes needed for visualization

CellTrek

  1. Download the CellTrek sample data from their Dropbox and put them into the data folder:
    1. scRNA-seq data: https://www.dropbox.com/s/ruseq3necn176c7/brain_sc.rds?dl=0
    2. ST data: https://www.dropbox.com/s/azjysbt7lbpmbew/brain_st_cortex.rds?dl=0
  2. Open R, write renv::restore(). If it asks you: Would you like to activate this project before restore? [Y/n], click Y and install all dependencies.
  3. Run celltrek_runs.R on a server to obtain the results
  4. Follow celltrek.Rmd for visualization

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