About This Vignette | Setup | Preparations | curatedMetagenomicsData | Metadata | Taxonomic Profiles | mOTUs2 Profiles | SIAMCAT Workflow (without Confounders) | The SIAMCAT Object | Filtering | Association Plot | Confounder Analysis | Machine Learning Workflow | Model Evaluation Plot | Model Interpretation Plot | Country Confounder | Association Testing | Machine Learning | Session Info

Introduction | Load the Data | Model Building on the French Dataset | Preprocessing | Model Training | Predictions | Application on the Holdout Dataset | Frozen Normalization | Holdout Predictions | Model Evaluation | Session Info

About This Vignette | Setup | Compare Associations | Compute Associations with SIAMCAT | Plot Heatmap for Interesting Genera | Study as Confounding Factor | ML Meta-analysis | Train LASSO Models | Investigate Feature Weights | Session Info

About This Vignette | Setup | Supervised Feature Selection | Load the Data | Train Model without Feature Selection | Incorrect Procedure: Train with Supervised Feature Selection | Correct Procedure: Train with Nested Feature Selection | Plot the Results | Naive Splitting of Dependent Data | Train with Naive Cross-validation | Train with Blocked Cross-validation | Apply to External Datasets | Session Info

About This Vignette | Introduction | Quick Start | Association Testing | Confounder Testing | Model Building | Data Normalization | Prepare Cross-Validation | Model Training | Make Predictions | Model Evaluation and Interpretation | Evaluation Plot | Interpretation Plot | Session Info

Introduction | Loading your data into R | SIAMCAT input | Features | Metadata | Label | LEfSe format files | metagenomeSeq format files | BIOM format files | Creating a siamcat object of a phyloseq object | Creating a siamcat-class object | phyloseq, label and orig_feat slots | All the other slots | Accessing and assigning slots | Slots inside the slots | Session Info