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 | Input data | Constructing the two GRMs | Full GRM | Sparse GRM | Fitting the null model | Defining variant sets | Set-based association tests | Burden | SKAT | ACAT-V | ACAT-O | Choosing a test | Practical recommendations | Session Information | References | See also

Introduction | Installation | Workflow | Preparing SNP data for the genetic relationship matrix | Fitting the null model | P-value calculations | Manhattan and QQ plots for p-values | GPU Acceleration (Optional) | Session Information | References | See also

Introduction | Input data requirements | Example | Fitting the null model | Sanity check against coxph() | Single-variant association tests | Kaplan-Meier curve for the top variant | Set-based (aggregate) tests | Session Information | References | See also

Introduction | Installation | Examples | Small Datasets | Large Datasets | Benchmarks | Test Datasets | R Codes in the Benchmark | Memory Usage and Elapsed Time | Miscellaneous | Save SCArrayAssay | Multicore or Multi-process Implementation | Downgrade SCArrayAssay | Conversion from Seurat to SingleCellExperiment | List of supported functions | Debugging | Session Information

Introduction | Workflow & Data Structure | Key Functions in SCArray | Example: Small-size Dataset | Example: Large-size Dataset (1.3M mouse brain cells) | Discussion | Acknowledgements

Introduction | Installation | Format conversion | Conversion from SingleCellExperiment | Conversion from a matrix | Examples | Data Manipulation and Analysis | 1. Row and Column Summarization | 2. PCA analysis | 3. UMAP analysis | Miscellaneous | Debugging | Session Information