Introduction | From aGDS to annotation GDS files | Relation to other Bioconductor packages | Key functions | Installation | Inspecting an annotation GDS file | Annotating variants | From a character vector of variant IDs | From a data.frame | From a GRanges object | From a VCF file or a VCF object | Whole-genome annotation with one file per chromosome | Writing annotations into a SeqArray GDS file | Converting annotation sources to GDS | gnomAD | Ensembl VEP | SnpEff | Summarising annotations | Counting unique values | Summary report | Session information

Introduction | Installation | Supported URL Schemes | Quick Start | Authentication | HTTP/HTTPS | Amazon S3 | S3-compatible services | Google Cloud Storage | Azure Blob Storage | Short-lived tokens: token provider functions | URL-specific credentials | Cache Control | Integration with SeqArray | Session Information

Introduction | Installation | Quick Start | Locate example files | Read variant information | Convert PGEN to GDS | Explore the GDS file | Access genotype data | Advanced Usage | Selecting a subset of variants | Importing a range with start/count | Parallel conversion | Conversion from GDS to PGEN | Integration with Bioconductor | Cleanup | Session Info

Overview | Parallel Computing | Application Program Interface (API) | Preparing Data | Data Format used in SeqArray | Format Conversion from VCF Files | Export to VCF Files | Modification | Data Processing | Functions for Data Analysis | Get Data | Apply Functions Over Array Margins | Apply Functions in Parallel | Examples | The performance of seqApply | Missing Rates for Variants | seqApply | C++ Integration | seqBlockApply | seqBlockApply + Parallel | seqMissing | Missing Rates for Samples | Allele Frequency | seqAlleleFreq | Principal Component Analysis | Multi-process Implementation | Individual Inbreeding Coefficient | Resources | Session Information | References

Benchmarks on building the training models | 1) Speedup factor using small training sets | 2) Speedup factor using medium training sets | 3) Speedup factor using large training sets | Multithreading | Session Info | References

Overview | Features | Examples | Pre-fit HIBAG Models for HLA Imputation | Build a HIBAG Model for HLA Genotype Imputation | Build and Predict in Parallel | Evaluate Overall Accuracy, Sensitivity, Specificity, etc | Evaluation in Figures | Report in Text | Report in Markdown | Report in LaTeX | Release HIBAG Models without Confidential Information | Release a Collection of HIBAG Models | Resources | Session Info | References

Overview | Association Tests | Allelic Association | Amino Acid Association | Resources | Session Info | References

SeqArray Functions | Key R Functions | Calculating Allele Frequencies | PCA R Implementation | Parallel Implementation | Bioconductor Features | GRanges and GRangesList | VariantAnnotation | Integration with SeqVarTools | Linear Regression | Integration with SNPRelate | LD-based Marker Pruning | Principal Component Analysis | Relatedness Analysis | Identity-By-State Analysis | Fixation Index ($F_\text{st}$) | GENESIS | Resources | Session Information | References

Introduction | Methods | Methods -- Advantages | Methods -- File Contents | Methods -- Key Functions | Benchmark | Benchmark -- Test 1 (sequentially) | Benchmark -- Test 2 (in parallel) | Benchmark -- Test 3 (C++ Integration) | Conclusion | Resource | Acknowledgements

Introduction | Installation of the package gdsfmt | High-level R functions | Creating a GDS file and variable hierarchy | Writing Data | R function add.gdsn | R function write.gdsn | R function append.gdsn | R function assign.gdsn | Create a large-scale data set | Reading Data | Subset reading read.gdsn and readex.gdsn | Apply a user-defined function marginally | Examples | Output to a text file | Transpose a matrix | Floating-point number vs. packed real number | Limited random-access of compressed data | Sparse Matrix | Checksum for Data Integrity | Stylish Terminal Output in R | Session Information

Overview | Installation of the package SNPRelate | Preparing Data | Data formats used in SNPRelate | Create a GWAS SNP GDS File | Using snpgdsCreateGeno() | Using the gdsfmt package | Format conversion from PLINK text/binary files | Format conversion from VCF files | Format conversion from VCF files using SeqArray | Data Analysis | LD-based SNP pruning | Principal Component Analysis (PCA) | $F_{st}$ Estimation | Relatedness Analysis | Estimating IBD Using PLINK method of moments (MoM) | Estimating IBD Using Maximum Likelihood Estimation (MLE) | Relationship inference Using KING method of moments | Identity-By-State Analysis | Integration with SeqArray | Function List | Resources | Session Information | References | Acknowledgements