Overview | Example data | Querying basics | Adding filters | Export to an annotated re-indexed sparse matrix | Export to Seurat

Overview | Example data | Advanced usage: dataframes with non-standard index columns | Advanced usage: using resize at the dataframe/array level

What is S4? | The S4 class system | A different world | S4 in Bioconductor | S4 from an end-user point of view | Where do S4 objects come from? | How to manipulate S4 objects? | How to find the right man page? | Inspecting objects and discovering methods | Implementing an S4 class (in 4 slides) | Class definition and constructor | Getters | Extending an existing class | Slot inheritance | Method inheritance | Incremental validity method | What else?

Overview | Example data | SOMA DataFrame | Slicing | Selecting columns | Filtering | SOMA SparseNDArray

Example data | SOMAExperiment | SOMADataFrame | SOMACollection | SOMAMeasurement | SOMASparseNDArray

Advanced schema configuration

Introduction | Installation | The Array virtual class | The extract_array() generic function | Block processing of array-like objects | Other functionalities | Session information

Introduction | Install and load the package | The SparseArray virtual class and its two concrete subclasses | SVT_SparseArray objects | Construction | SVT_SparseArray vs COO_SparseArray | The SparseArray API | The core array API | type() and is_sparse() | is_nonzero() and the nz*() functions | Subsetting and subassignment | Summarization methods (whole array) | Operations from the Arith, Compare, Logic, Math, Math2, and Complex groups | The 2D API | SVT_SparseMatrix objects | Transposition | Combine multidimensional objects along a given dimension | matrixStats methods | rowsum() and colsum() | Matrix multiplication and cross-product | Other operations | Generate a random SVT_SparseArray object | Read/write a sparse matrix from/to a CSV file | Comparison with dgCMatrix objects | "SVT layout" vs "CSC layout" | Working with a big sparse dataset | Learn more | Session information

Motivation and challenges | Memory footprint | RleArray and HDF5Array objects | Hands-on | DelayedArray/HDF5Array: Future developments

Introduction | Implementing the seed class | Class definition | Constructor | The seed contract | dim() and dimnames() | extract_array() | What to import? | Testing | Implementing high-level classes ADSArray and ADSMatrix | ADSArray class definition | The ADSArray() constructor | ADSMatrix class definition | Going from ADSArray to ADSMatrix | Going from ADSMatrix to ADSArray | Implementing optimized backend-specific methods | What to export?

Recent additions to package DelayedArray | Recent additions to package HDF5Array | Work in progress and future work

Introduction | Vector-like and list-like objects | Vector-like objects | Subsetting a vector-like object | Concatenating vector-like objects | Looping over subsequences of vector-like objects | List-like objects | Vector Annotations | Session Information

Package remotes | GitHub | Other sources | CRAN submission

1 Introduction | 2 IRanges objects | 3 Vector Views | 4 Lists of Atomic Vectors | 5 Session Information