Installation | Introduction | Relationship to existing Bioconductor packages | Introducing ReducedExperiment containers with a case study | The case study data | Applying factor analysis | Module analysis | Identifying factor and module associations | Finding functional enrichments for factors and modules | Applying factors and modules to new datasets | Factor projection | Applying modules to new data | Module preservation | Extending the ReducedExperiment class | Constructing a ReducedExperiment from scratch | Vignette references | Session Information

Introduction | Getting Started | R Package Dependencies | Command Line Dependencies | Searching for Potential Transposable Elements using packFinder | Getting Data | Using packSearch | Analysing Potential Transposable Elements using packFinder | Clustering of Transposable Elements | Reading VSEARCH Output Files | Clustering of TIR Sequences | Alignment of Transposable Elements | BLAST Analysis | Data Formats and Conversion | packSearch Dataframe | GRanges | FASTA | Step-wise packSearch Functions | Identifying Potential TIRs | Obtaining TSD Sequences | Filtering TIR Matches | Get Transposon Sequences | References | Session Information