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Available cell type markers

Source: R/markers.R
clustermole_markers.Rd

Retrieve cell type markers from the clustermole database.

Usage

clustermole_markers(species = c("hs", "mm"))

Arguments

species

Gene symbol species: hs for human or mm for mouse.

Value

A data frame of cell type markers with these columns:

  • gene: Canonical gene symbol for the requested species.

  • gene_original: Original source gene symbol.

  • celltype_full: Full cell type signature identifier.

  • db: Source database.

  • celltype: Cell type label.

  • organ: Organ label.

  • species: Source signature species, if known.

  • n_genes: Gene count per signature.

Details

The gene column uses the official NCBI symbols for the requested species. The package maps the aliases in each source database to these symbols. The gene_original column preserves the symbol from the source. The source databases include both human and mouse cell type markers. The package maps them across species with ortholog data from the Alliance of Genome Resources and keeps only reciprocal best matches. The output does not include genes that have no ortholog in the requested species and does not include signatures with fewer than five genes.

Examples

markers <- clustermole_markers()
head(markers)
#> # A tibble: 6 × 8
#>   celltype_full         db    species organ celltype gene_original gene  n_genes
#>   <chr>                 <chr> <chr>   <chr> <chr>    <chr>         <chr>   <int>
#> 1 (Pro-) Subiculum | H… ScTy… ""      Hipp… (Pro-) … ADAMTS2       ADAM…      10
#> 2 (Pro-) Subiculum | H… ScTy… ""      Hipp… (Pro-) … FN1           FN1        10
#> 3 (Pro-) Subiculum | H… ScTy… ""      Hipp… (Pro-) … KLHL1         KLHL1      10
#> 4 (Pro-) Subiculum | H… ScTy… ""      Hipp… (Pro-) … LIPM          LIPM       10
#> 5 (Pro-) Subiculum | H… ScTy… ""      Hipp… (Pro-) … NPSR1         NPSR1      10
#> 6 (Pro-) Subiculum | H… ScTy… ""      Hipp… (Pro-) … NTS           NTS        10