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Seurat.IntegrateData Tutorial 📝

This tutorial is based off the Integration and Label Transfer Vignette published and developed by the Satija Lab.

  1. git clone our Seurat.IntegrateData repository onto your local machine
  2. Open up your computer's Terminal and cd into the same directory as your git clone folder's location. You can also use a graphical interface to navigate to the correct working directory.
  3. Once in the correct directory, cd into the /src folder and run the following command: Rscript batch_correction.R --input_files demo.txt --use_filenames_for_plots FALSE --ncomps 50 --nCount_RNA TRUE --nFeature_RNA TRUE --output_file_name hnscc_and_mel_bc
    • demo.txt contains the file paths for 2 test datasets within the /data directory -- HNSCC_noribo_small.txt and MEL_noribo_small.txt. These are 500x500 single-cell cancer datasets that will be batch-corrected
    • We utilize several command line flags to provide our users with the freedom to customize their batch correction output
    • To read further about each Command Line Flag / Parameter, take a look at the technical documentation for our module here -> Link
  4. You will now have 3 output files: batch_correction_log.txt, hnscc_and_mel_bc.rds, and hnscc_and_mel_bc.pdf
    • The .txt file contains a log of each process carried out during the batch correction script's execution
    • The .rds file can be used on another one of GenePattern's Seurat suite modules, such as the Seurat.Clustering module
    • The .pdf file contains UMAP plots and Violin plots of the integrated HNSCC and MEL datasets