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README.md

File metadata and controls

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Example input files are as follows.

  • example_train_metadata.txt: the clinical metadata of the training dataset, including experimental group, cohort, and other metadata indices.
  • example_train_abundance.txt: the microbial abundance profile of the training dataset.
  • example_test_metadata.txt: the clinical metadata of the external test dataset.
  • example_test_abundance.txt: the microbial abundance profile of the external test dataset.
  • example_other_metadata.txt: the clinical metadata of samples with other diseases used to assess the specificity of identified markers.
  • example_other_abundance.txt: the microbial abundance profile of samples with other diseases.
  • covariates.txt: the example input covariates file for Step 4.
  • convert.tsv: the example converted microbial count matrices for Step 11.

Example results are as follows.

  • differential_plot.pdf: the volcano plot of differential signatures (output file of Step 4).
  • cross_validation_auc.pdf: the visualization of the cross-validation AUC of the best-performing model constructed in Step 7.
  • validation_AUC.pdf: the visualization of performance metrics of markers in internal validations (output file of Step 8).
  • marker_importance.pdf: the visualization of permutation feature importance of candidate markers in the best-performing model (output file of Step 10).