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DendrouLab / panpipes-tutorials

tutorials to run panpipes
BSD 3-Clause "New" or "Revised" License
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Error in the pre-filled Preprocess pipline.yml file #50

Open andrewkcleeuc opened 5 months ago

andrewkcleeuc commented 5 months ago

For the section "Filtering data with panpipes - running the pipeline"

The pre-filled pipeline.yml file (here) contains an error on the specificed ATAC normalisation method, and needs to be updated. 

# ATAC preprocessing steps
# ------------------------
atac:
  binarize: False
  normalize: TFIDF  #"log1p" or "TFIDF"

The figures generated using this pre-filled pipeline.yml do not match the PCA plot images posted in the documentation. This is because the pre-filled YAML file uses TFIDF, but the plot images were generated using log1p .