Overview | Data Preparation | Creating Test Data with Synthetic Chimeras | Comparing Detection Methods | Helper function for benchmarking | Run benchmarks | Benchmark Summary Table | Analyzing Missed Chimeras | Comparing Detection Across Different Chimera Types | Summary Table: All Scenarios | Visualizing Results | Effect of Chimera Abundance on Detection | Abundance Summary Table | Visualizing Abundance Effect | Effect of Parent Sequence Distance

The detect-then-filter design | A first detector | Removing flagged taxa | Combining detectors | Diagnostics | Negative-control classification | Abundance-, sequence-, and chimera-based detectors | Control-based decontamination (a different tool)

Taxonomy format overview | Prefix-based formats | UNITE format (k__/p__ prefixes) | SINTAX / UTAX format | Greengenes2 format (d__/p__ prefixes) | Positional formats | Unprefixed semicolon-delimited (generic) | PR2 format (no prefixes, 9 levels) | Sequence name placement | Working with taxonomy formats in dbpq | Detecting the format | Getting rank information | Summarizing databases | Listing ranks | Converting between formats | Downloading databases in specific formats | Database formats and classification algorithms | Choosing a database and classifier

Introduction | Installation | Basic Usage | Calculating Carbon Footprint | Understanding the Results | Location-Specific Carbon Intensity | Hardware Configuration | Current R Session Footprint | Visualization with Reference Values | Best Practices | Next Steps | References

Introduction | Setup | Basic targets Integration | Simple Example | Advanced Pipeline Analysis | Comparing Different Configurations | Visualizing Pipeline Carbon Footprint | Target-Level Analysis | Best Practices for Sustainable Pipelines | Integration with Workflow | Conclusion | References

Custom functions in filter | Custom functions in mutate | Occurrence-level transformations | Complex pipelines

Overview | Filter samples | Filter taxa | Mutate | Select columns | Chaining operations

Introduction to MiscMetabar: an R package to facilitate visualization and reproducibility in metabarcoding analysis | Raison d'être | Quick overview | Summarize a physeq object | Create an interactive table of the tax_table | Sankey diagram of the tax_table | Upset plot for visualize distribution of taxa in function of samples variables | References | Session inform