data-raw/pbmc3k_markers.R

In robertamezquita/Inkwell: Containers for Curated Cell Type Signatures

library(GSEABase)

cd4_t_cells <- GeneSet(
    setName = 'CD4 T cells',    
    type = SymbolIdentifier('org.Hs.eg.db'),
    organism = 'Homo sapiens',    
    geneIds = 'IL7R',
    urls = 'https://satijalab.org/seurat/pbmc3k_tutorial.html',
    contributor = 'Robert A. Amezquita'
)

cd14_monocytes <- GeneSet(
    setName = 'CD14+ Monocytes',    
    type = SymbolIdentifier('org.Hs.eg.db'),
    organism = 'Homo sapiens',    
    geneIds = c('CD14', 'LYZ'),
    urls = 'https://satijalab.org/seurat/pbmc3k_tutorial.html',
    contributor = 'Robert A. Amezquita'
)

b_cells <- GeneSet(
    setName = 'B cells',    
    type = SymbolIdentifier('org.Hs.eg.db'),
    organism = 'Homo sapiens',    
    geneIds = 'MS4A1',
    urls = 'https://satijalab.org/seurat/pbmc3k_tutorial.html',
    contributor = 'Robert A. Amezquita'
)

cd8_t_cells <- GeneSet(
    setName = 'CD8 T cells',    
    type = SymbolIdentifier('org.Hs.eg.db'),
    organism = 'Homo sapiens',    
    geneIds = 'CD8A',
    urls = 'https://satijalab.org/seurat/pbmc3k_tutorial.html',
    contributor = 'Robert A. Amezquita'
)

fcgr3a_monocytes <- GeneSet(
    setName = 'FCGR3A+ Monocytes',    
    type = SymbolIdentifier('org.Hs.eg.db'),
    organism = 'Homo sapiens',    
    geneIds = c('FCGR3A', 'MS4A7'),
    urls = 'https://satijalab.org/seurat/pbmc3k_tutorial.html',
    contributor = 'Robert A. Amezquita'
)

nk_cells <- GeneSet(
    setName = 'NK cells',    
    type = SymbolIdentifier('org.Hs.eg.db'),
    organism = 'Homo sapiens',    
    geneIds = c('GNLY', 'NKG7'),
    urls = 'https://satijalab.org/seurat/pbmc3k_tutorial.html',
    contributor = 'Robert A. Amezquita'
)

dendritic_cells <- GeneSet(
    setName = 'Dendritic cells',    
    type = SymbolIdentifier('org.Hs.eg.db'),
    organism = 'Homo sapiens',    
    geneIds = c('FCER1A', 'CST3'),
    urls = 'https://satijalab.org/seurat/pbmc3k_tutorial.html',
    contributor = 'Robert A. Amezquita'
)

megakaryocytes <- GeneSet(
    setName = 'Megakaryocytes',    
    type = SymbolIdentifier('org.Hs.eg.db'),
    organism = 'Homo sapiens',    
    geneIds = c('PPBP'),
    urls = 'https://satijalab.org/seurat/pbmc3k_tutorial.html',
    contributor = 'Robert A. Amezquita'
)

pbmc3k_markers <- GeneSetCollection(
    list(
        cd4_t_cells, cd8_t_cells,
        b_cells,
        cd14_monocytes, fcgr3a_monocytes,
        nk_cells, dendritic_cells,
        megakaryocytes
    )
)

usethis::use_data(pbmc3k_markers, overwrite = TRUE)