Introduction | Scope of package | OWL interface | Methods | Conceptual overview of ontology with cell types | Illustration in a single-cell RNA-seq dataset | Labeling PBMC in the Seurat tutorial | Relationships asserted in the Cell Ontology | Subsetting SingleR resources using ontological mapping | A data.frame mapping from informal to formal terms | Binding formal tags to the HPCA data | Subsetting using the class hierarchy of Cell Ontology | Visually identifying differences between ontology versions for a set of given terms | Disease concept relationships | Related tools | Illustration with a phenotype ontology | References

Introduction | Illustration with Human Phenotype ontology

Motivation | HTSlib version | Use | Find headers | Compile and link against the library | Implementation notes

Data | Clustering | Generative classifier

OHCA

Introduction | Comparing old and new | A quick tour | The eSet object: high-throughput experiments | assayData: high-throughput data | phenoData: sample covariates | featureData: feature covariates | experimentData: experiment description | annotation: assay description | Important eSet methods | Additional eSet methods | Subclasses of eSet | ExpressionSet | MultiSet and SnpSet | Comments on assayData: high-throughput data storage | Extending eSet | Implementing a new class: a SwirlSet example | Versioned | Versioned versus VersionedBiobase | Adding Versioned information to your own classes | Summary | Session Information

A note on esApply | Session Information