This R package was made to have an easy access through R to our cell type marker database (created by Nils).
The easiest way to install the package is using devtools.
devtools::install_github("klprint/markerDB")First, we access the MarkerDB and see what species are already available:
getSpecies()[1] "mouse" "human"
Next, we can get some informations what celltypes are already annotated in a specific species:
getSpeciesInfo("mouse")
$celltypes
[1] "neural_stem_cell" "GABAergic_interneurons" "glial_progenitor" "undifferentiated_spermatogonia" "stem_cell"
[6] "spermatogonial_stem_cell" "GABAergic_progenitors" "hematopoietic_stem_cells" "differentiating_neurons" "newly_born_neurons"
[11] "medulloblastomas" "spermatogonia" "quiescent_hematopoietic_stem_cells" "Astrocytes" "Oligodendrocytes"
[16] "neuronal_progenitors" "primordial_germ_cells" "sertoli_cells" "leydig_cells" "spermatocytes"
[21] "round_spermatids" "condensing_spermatids" "condensed_spermatids" "elongating_spermatids" "adipose-derived_stem_cell"
[26] "white_fat_cell" "cancer_stem_cell" "alveolar_macrophage" "tumor_endothelial_cell" "anterior_foregut_endoderm_cell"
[31] "cd4+_t_follicular_helper_cell" "hematopoietic_stem_cell" "dendritic_cell" "mesenchymal_stem_cell" "endothelial_progenitor_cell"
[36] "m2_macrophage" "rod_photoreceptor_precursor_cell" "pluripotent_stem_cell" "peripheral_monocyte" "rhombic_lip_cell"
[41] "prostate_stem_cell" "prostate_progenitor_cell" "enteroendocrine_cell" "epithelial_cell" "endothelial_cell"
[46] "endometrial_precursor_cell" "beta_cell" "neuron" "oligodendrocyte" "astrocyte"
[51] "microglial_cell" "amacrine_cell" "retinal_ganglion_cell" "hematopoietic_cell" "tympanic_border_cell"
[56] "oogonial_stem_cell" "sinoatrial_node_cell" "intestinal_stem_cell" "colonic_stem_cell" "neutrophil"
[61] "macrophage" "monocyte" "submandibular_gland_stem_cell" "side-population_cell" "paneth_cell"
[66] "hematopoietic_progenitor_cell" "small_intestinal_stem_cell" "testicular_stem_cell" "skeletal_muscle_stem_cell" "heart_muscle_stem_cell"
[71] "mesenchymal_progenitor_cell" "ng2-glia_cell" "outer_pillar_cell" "stromal_cell" "luminal_epithelial_cell"
[76] "basal_epithelial_cell" "cd4+_t_cell" "brown_fat_cell" "beige_fat_cell" "cardiac_progenitor_cell"
[81] "chondrocyte-derived_bone_cell" "liver_progenitor_cell" "pancreatic_progenitor_cell" "atrial_cell" "ventricular_compact_cell"
[86] "ventricular_trabecular_cell" "epithelial_progenitor_cell" "progenitor_cell" "tumor-propagating_cell" "erythroid_progenitor"
[91] "clara_cell" "leukocyte" "pancreatic_stem_cell" "quiescent_small_intestinal_stem_cell" "ito_cell_(hepatic_stellate_cell)"
[96] "eosinophil" "dermal_fibroblast" "ventricular_cardiomyocyte" "airway_dendritic_cell" "hair_cell"
[101] "pericyte" "naive_thymic_nkt17_cell" "liver_stem_cell" "myofibroblast" "stem_leydig_cell"
[106] "glomus_cell" "olfactory_sensory_neuron" "vomeronasal_sensory_neuron" "cancer_cell" "lipofibroblast"
[111] "mesothelial_cell" "goblet_cell" "type_ii_pneumocyte" "neuroendocrine_cell" "germ_cell"
[116] "embryonic_stem_cell" "cardiomyocyte" "lymphatic_endothelial_cell" "inflammatory_cell" "muscle_satellite_cell"
[121] "alpha_cell" "b_cell" "t_cell" "basophil" "megakaryocyte"
[126] "mesenchymal_stromal_cell" "m1_macrophage" "fat_cell_(adipocyte)" "immature_neuron" "radial_glial_cell"
[131] "neuroblast" "basal_cell" "osteocyte" "osteogenic_cell" "osteoclast"
[136] "mesenchymal_cell" "erythroid_precursor" "hair_follicle_cell" "myeloid_cell" "platelet"
[141] "fibroblast" "smooth_muscle_cell" "matrix_fibroblast" "immune_cell" "lymphocyte"
[146] "cxcr6+_t_cell" "granulocyte" "natural_killer_cell" "cd8+_t_cell" "hormone_sensing_progenitor"
[151] "hormone_sensing_differentiated_cell" "luminal_progenitor" "differentiated_alveolar_cell" "alveolar_progenitor_cell" "myoepithelial_cell"
[156] "procr+_basal_cell" "early_enterocyte_precursor_cell" "transit_amplifying_(ta)_cell" "late_enterocyte_precursor_cell" "enterocyte"
[161] "enteroendocrine_precursor_cell" "brush_cell_(tuft_cell)" "oligodendrocyte_precursor_cell" "mural_cell" "plasmacytoid_dendritic_cell"
[166] "erythroid_cell" "hepatocyte"
$ensembl
[1] "mmusculus_gene_ensembl"
$latin
[1] "Mus musculus"
$name
[1] "mouse"
Let's say we then want to find all cell types in mouse cerebellum. We can use the following to get a vector of cell types:
getAllCelltypesInTissue("cerebellum", "mouse")[1] "neural_stem_cell" "GABAergic_interneurons" "glial_progenitor" "GABAergic_progenitors" "medulloblastomas" "Astrocytes" "Oligodendrocytes" "neuronal_progenitors" "rhombic_lip_cell"
But here, all cell types throughout development are listed. If we are only interested in cell types, already annotated in P7 cerebellum, we can extend the querry with a list:
getAllCelltypesInTissue("cerebellum", "mouse", filter_list = list(stage = "P7"))[1] "neural_stem_cell" "Astrocytes" "Oligodendrocytes" "neuronal_progenitors"
And finally, we can find marker genes for neural stem cells:
getMarkerGenes("neural_stem_cell", "mouse")[1] "ENSMUSG00000004891" "ENSMUSG00000029086" "ENSMUSG00000005320" "ENSMUSG00000030283" "ENSMUSG00000020122" "ENSMUSG00000074637"
And markers for neural stem cells at stage P7:
getMarkerGenes("neural_stem_cell", "mouse", filter_list = list(stage="p7"))[1] "ENSMUSG00000029086"
And whoever does not like ENSEMBL IDs can also get the gene symbols:
getMarkerGenes("neural_stem_cell", "mouse", filter_list = list(stage="p7"), field = "marker_name")[1] "Prom1"