Welcome to sourcepredict’s documentation!

Homepage: github.com/maxibor/sourcepredict

Contents:

• Introduction
• Installation
• Usage
  • Running sourcepredict on the test dataset
  • Command line interface
  • Command line arguments
  • Choice of the taxonomic classifier
• Output
  • SourcePredict result file
  • Embedding csv file
• Methods
  • Prediction of unknown sources proportion
  • Prediction of known source proportion
  • Combining unknown and source proportion
• Custom sources
  • Pipeline installation
  • Running the pipeline
• Adding new sources to an existing source file
• Sourcepredict example 1: Gut host species prediction
  • Preparing the data
  • Sourcepredict
  • Sourcetracker2
  • Conclusion
• Sourcepredict example2: Estimating source proportions
  • Preparing mixed samples
  • Sourcepredict
  • Sourcetracker2
  • Conclusion
• Sourcepredict example3: Segregating patients with or without Clostridium difficile infection (CDI) on the basis of 16s microbiome
  • Downloading data
  • Reading the results of the dada2-nf pipeline
  • Normalizing dataframes
  • Creating labels dataframe and response variable array
  • Exploring the dataset
  • Reading Sourcepredict results
• Comparing with Sourcetracker 2

Indices and tables

• Index
• Module Index
• Search Page