NSForest Documentation

Contents

• Installation
• Tutorial
  • Tutorial
    • Setting up environment
    • Data Exploration
      • Loading h5ad AnnData file
      • Defining cluster_header as cell type annotation.
      • Defining output_folder for saving results
      • Looking at sample labels
      • Looking at genes
      • Checking cell annotation sizes
    • Preprocessing
      • Generating scanpy dendrogram
      • Calculating cluster medians per gene
      • Calculating binary scores per gene per cluster
      • Plotting median and binary score distributions
      • Saving preprocessed AnnData as new h5ad
    • Running NS-Forest
      • Plotting classification metrics from NS-Forest results
    • Plotting scanpy dot plot, violin plot, matrix plot for NS-Forest markers
    • Evaluating input marker list
      • Getting marker list in dictionary format: {cluster: marker_list}
      • Plotting classification metrics from marker evaluation
    • Plotting scanpy dot plot, violin plot, matrix plot for input marker list
• Preprocessing
  • dendrogram()
  • prep_medians()
  • get_medians()
  • prep_binary_scores()
• NSForest
  • NSForest()
• Evaluating
  • DecisionTree()
  • add_fraction()
• Plotting with scanpy
  • dotplot()
  • stackedviolin()
  • matrixplot()
• Plotting with plotly
  • boxplot()
  • scatter_w_clusterSize()
• Utility Functions
  • str_to_list()
  • prepare_markers()