Introduction | AbSeq core analyses | Installation | Bioconductor | GitHub | System prerequisites | R package dependencies | Quick start | Datasets | Basic analysis | HTML reports' directory structure | Comparative analysis using multiple datasets | Advanced Examples | Lazy loading | Alternative reporting options | Parallelization | Interpretation of report's figures | Sequence quality analysis | Sequence length | Alignment quality | Insertions, deletions, and mismatches | Abundance and association analysis | V-(D)-J germline abundance | V-J germline associations | Productivity analysis | V-J frameshifts | Stop codons | Indels and mismatches | Diversity analysis | Clonotype-based analysis | Spectratype analysis | Position-specific analysis | Comparative analysis | Over-representation analysis | Overlapping analysis | Multi-sample analysis | Two-sample analysis | Correlation analysis | Clustering analysis | Appendices | Datasets | Session Info | References

1 Introduction | 2 Citation | 3 Installation instructions | 4 Quick start | 5 S4 classes and methods | 6 Ensemble of Gene Set Enrichment Analysis | 7 EGSEA report | 8 EGSEA on a non-human dataset | 9 EGSEA on a count matrix | 10 EGSEA on a list of genes | 11 Non-standard gene set collections | 12 Adding new GSE method | 13 Packages used | References