Introduction | Installation | Bioconductor install | GitHub install | Input Data | Transductomics data | Pileup files | TrIdentClassifier() | Function components | Contig filtering | Changing pileup windowSize | Pattern-matching | Patterns | Sloping: | Prophage-like: | noPattern: | Highly active/abundant and heterogenously integrated/present Prophage-like elements | NoPattern classifications with high VLP-fraction:whole-community read coverage ratios | Usage | Arguments/Parameters | Output | plotTrIdentResults() | Re-building pattern-matches | Plotting read coverage and associated pattern-matches | specializedTransductionID() | Zoom-in on Prophage-like elements | Identify borders of Prophage-like elements | Search for specialized transduction outside Prophage-like borders | geneSearch() | Search for gene annotations | Plot gene annotation locations | Arguments/parameters | Supplemental information | Usage Note | Acknowledgments | Funding | Session Information

Introduction | Installation | CRAN install | GitHub install | Input data | Pileups | gff TSV | ProActiveDetect() | Function components | Chunking | Filtering | Changing pileup windowSize | Pattern-matching | Elevation pattern: | Gap pattern: | Elevation/Gap pattern: | noPattern: | Calculating elevation ratios | Extracting gene annotations in elevated/gapped regions | Usage | Arguments/parameters | Output | plotProActiveResults() | Re-building pattern-matches | Plotting read coverage and associated pattern-matches | View select metagenome plots | View select genome plots | geneAnnotationSearch() | Search for gene annotations | Plot gene annotation locations | Supplemental information | Funding | Session Information