Building Trees from Taxonomies2 months ago
Checking that that the induced tree is correct | Introducing a missing root node | Skipping over missing taxonomic assignments | Avoiding duplicated names across different taxonomic levels
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Cell-type Hierarchy Informs COVID-19 Immunology2 months ago
The effect of a high-fat high-sugar (HFHS) diet on the mouse microbiome2 months ago
Overview | Why phylogeny-aware plots? | Setup | Taxonomy-based tree construction | Diet contrasts on day 7 | Interpretation | Longitudinal trajectories within HFHS | Interpretations | Alternative Sorting | Session Info
Getting Started2 months ago
Overview | Installation | Quick Start | Vignettes | Workflow Vignettes | Building Trees from Taxonomies | Customizing Style | Exporting Views | Runtime Evaluation | Case-Study Vignettes | HFHS Diet and the Mouse Microbiome | Atlas 1006 — Tipping Points in the Human Gut | Diet Analysis with DESeq2 Normalization | Global Patterns — phyloseq and TreeSummarizedExperiment | COVID-19 Immunology — Beyond Microbiome Data | Function Reference | Contact
Customizing Style in phylobar2 months ago
Overview | Color Palette | Widget Size | Sample Label Styling | Tree-bar Layout Ratio | Legend Placement | Optional Hierarchical Reordering | Session Info
Exporting to Vector Graphics Format2 months ago
Introduction | Step 1: Exporting from Browser | Step 2: Open in Editor | Step 3: Modify and Save
Working with phyloseq and TreeSummarizedExperiment versions of the Global Patterns Dataset2 months ago
Setup | phyloseq Inputs | Phylogenetic Tree Tree | Using Taxonomic Hierarchy | TreeSummarizedExperiment Inputs
Tipping Points in the Atlas 1006 Dataset2 months ago
Setup | Interpretation | Session Info
Differences in the Community Composition due to Diet2 months ago
Setup | Interpretation | Session Info
The Mindfulness Study1 years ago
Evaluating Effects | Model Alterations | Synthetic Null Testing | Random Forests | Bootstrap
Illustration with Nonlinear Effects2 years ago
Microbiome - Metabolome Mediation Analysis2 years ago
Data Processing | Lasso Approach | Hurdle-Lognormal Approach
Quick Start with Random Data2 years ago
Effect Estimates | Inference
Example on Simulated Data2 years ago
