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Cell-type marker database

Source: R/data.R
markerDB.Rd

A curated database of positive and negative cell-type marker genes for human and mouse, stored in sparse matrix format. This dataset is used internally by typoClust() for marker-based cell-type annotation.

Format

An object of class CelliVerse_Data, implemented as a named list with two elements:

human

A list containing human marker databases:

positive_db

An object of class CelliVerse_Sparse_Data wrapping a sparse dgCMatrix of dimensions 16,899 genes × 9,410 cell types.

negative_db

An object of class CelliVerse_Sparse_Data wrapping a sparse dgCMatrix of dimensions 329 genes × 93 cell types.

mouse

A list containing mouse marker databases:

positive_db

An object of class CelliVerse_Sparse_Data wrapping a sparse dgCMatrix of dimensions 4,779 genes × 2,112 cell types.

negative_db

An object of class CelliVerse_Sparse_Data wrapping a sparse dgCMatrix of dimensions 32 genes × 33 cell types.

Source

Curated from published cell-type marker resources and expert annotation.

Details

Rows correspond to marker genes and columns correspond to annotated cell types. Matrix values encode marker presence or strength as defined during database construction. Sparse representation is used to minimize memory usage.

See also

typoClust, markerDictionary, tissueCondition_types