From 791f58307e9a563867aedddd59bc64c18415af09 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 7 Jan 2025 14:51:46 -0600 Subject: [PATCH] keep original panglao name when creating reference --- .../consensus-cell-type-reference.tsv | 613 +++++++++--------- .../scripts/02-prepare-consensus-reference.R | 6 +- 2 files changed, 315 insertions(+), 304 deletions(-) diff --git a/analyses/cell-type-consensus/references/consensus-cell-type-reference.tsv b/analyses/cell-type-consensus/references/consensus-cell-type-reference.tsv index 18003c3d8..da7dcdc61 100644 --- a/analyses/cell-type-consensus/references/consensus-cell-type-reference.tsv +++ b/analyses/cell-type-consensus/references/consensus-cell-type-reference.tsv @@ -1,302 +1,311 @@ -panglao_ontology panglao_annotation blueprint_ontology blueprint_annotation_main blueprint_annotation_fine consensus_ontology consensus_annotation -CL:0000583 alveolar macrophage CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000767 basophil CL:0000775 Neutrophils Neutrophils CL:0000094 granulocyte -CL:0000771 eosinophil CL:0000775 Neutrophils Neutrophils CL:0000094 granulocyte -CL:0000235 macrophage CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000097 mast cell CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000576 monocyte CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000775 neutrophil CL:0000775 Neutrophils Neutrophils CL:0000775 neutrophil -CL:0000092 osteoclast CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000091 Kupffer cell CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000453 Langerhans cell CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000129 microglial cell CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000889 myeloid suppressor cell CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000874 splenic red pulp macrophage CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte -CL:0000767 basophil CL:0000576 Monocytes Monocytes CL:0000766 myeloid leukocyte -CL:0000451 dendritic cell CL:0000576 Monocytes Monocytes CL:0000113 mononuclear phagocyte -CL:0000771 eosinophil CL:0000576 Monocytes Monocytes CL:0000766 myeloid leukocyte -CL:0000097 mast cell CL:0000576 Monocytes Monocytes CL:0000766 myeloid leukocyte -CL:0000576 monocyte CL:0000576 Monocytes Monocytes CL:0000576 monocyte -CL:0000775 neutrophil CL:0000576 Monocytes Monocytes CL:0000766 myeloid leukocyte -CL:0000784 plasmacytoid dendritic cell CL:0000576 Monocytes Monocytes CL:0000113 mononuclear phagocyte -CL:0000889 myeloid suppressor cell CL:0000576 Monocytes Monocytes CL:0000766 myeloid leukocyte -CL:0000037 hematopoietic stem cell CL:0000050 HSC MEP CL:0008001 hematopoietic precursor cell -CL:0000038 erythroid progenitor cell CL:0000050 HSC MEP CL:0008001 hematopoietic precursor cell -CL:0000084 T cell CL:0000624 CD4+ T-cells CD4+ T-cells CL:0000084 T cell -CL:0002038 T follicular helper cell CL:0000624 CD4+ T-cells CD4+ T-cells CL:0000624 CD4-positive, alpha-beta T cell -CL:0000893 thymocyte CL:0000624 CD4+ T-cells CD4+ T-cells CL:0000084 T cell -CL:0000798 gamma-delta T cell CL:0000624 CD4+ T-cells CD4+ T-cells CL:0000084 T cell -CL:0000814 mature NK T cell CL:0000624 CD4+ T-cells CD4+ T-cells CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell CL:0000624 CD4+ T-cells CD4+ T-cells CL:0002419 mature T cell -CL:0000910 cytotoxic T cell CL:0000624 CD4+ T-cells CD4+ T-cells CL:0002419 mature T cell -CL:0000912 helper T cell CL:0000624 CD4+ T-cells CD4+ T-cells CL:0002419 mature T cell -CL:0000813 memory T cell CL:0000624 CD4+ T-cells CD4+ T-cells CL:0002419 mature T cell -CL:0000815 regulatory T cell CL:0000624 CD4+ T-cells CD4+ T-cells CL:0002419 mature T cell -CL:0000084 T cell CL:0000815 CD4+ T-cells Tregs CL:0000084 T cell -CL:0002038 T follicular helper cell CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000893 thymocyte CL:0000815 CD4+ T-cells Tregs CL:0000084 T cell -CL:0000798 gamma-delta T cell CL:0000815 CD4+ T-cells Tregs CL:0000084 T cell -CL:0000814 mature NK T cell CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000898 naive T cell CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000910 cytotoxic T cell CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000912 helper T cell CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000813 memory T cell CL:0000815 CD4+ T-cells Tregs CL:0002419 mature T cell -CL:0000815 regulatory T cell CL:0000815 CD4+ T-cells Tregs CL:0000815 regulatory T cell -CL:0000084 T cell CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000084 T cell -CL:0002038 T follicular helper cell CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000624 CD4-positive, alpha-beta T cell -CL:0000893 thymocyte CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000084 T cell -CL:0000798 gamma-delta T cell CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000084 T cell -CL:0000814 mature NK T cell CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell CL:0000904 CD4+ T-cells CD4+ Tcm CL:0002419 mature T cell -CL:0000910 cytotoxic T cell CL:0000904 CD4+ T-cells CD4+ Tcm CL:0002419 mature T cell -CL:0000912 helper T cell CL:0000904 CD4+ T-cells CD4+ Tcm CL:0002419 mature T cell -CL:0000813 memory T cell CL:0000904 CD4+ T-cells CD4+ Tcm CL:0000813 memory T cell -CL:0000815 regulatory T cell CL:0000904 CD4+ T-cells CD4+ Tcm CL:0002419 mature T cell -CL:0000084 T cell CL:0000905 CD4+ T-cells CD4+ Tem CL:0000084 T cell -CL:0002038 T follicular helper cell CL:0000905 CD4+ T-cells CD4+ Tem CL:0000624 CD4-positive, alpha-beta T cell -CL:0000893 thymocyte CL:0000905 CD4+ T-cells CD4+ Tem CL:0000084 T cell -CL:0000798 gamma-delta T cell CL:0000905 CD4+ T-cells CD4+ Tem CL:0000084 T cell -CL:0000814 mature NK T cell CL:0000905 CD4+ T-cells CD4+ Tem CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell -CL:0000910 cytotoxic T cell CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell -CL:0000912 helper T cell CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell -CL:0000813 memory T cell CL:0000905 CD4+ T-cells CD4+ Tem CL:0000813 memory T cell -CL:0000815 regulatory T cell CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell -CL:0000084 T cell CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000084 T cell -CL:0002038 T follicular helper cell CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000791 mature alpha-beta T cell -CL:0000893 thymocyte CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000084 T cell -CL:0000798 gamma-delta T cell CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000084 T cell -CL:0000814 mature NK T cell CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell -CL:0000910 cytotoxic T cell CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell -CL:0000912 helper T cell CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell -CL:0000813 memory T cell CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000813 memory T cell -CL:0000815 regulatory T cell CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell -CL:0000084 T cell CL:0000913 CD8+ T-cells CD8+ Tem CL:0000084 T cell -CL:0002038 T follicular helper cell CL:0000913 CD8+ T-cells CD8+ Tem CL:0000791 mature alpha-beta T cell -CL:0000893 thymocyte CL:0000913 CD8+ T-cells CD8+ Tem CL:0000084 T cell -CL:0000798 gamma-delta T cell CL:0000913 CD8+ T-cells CD8+ Tem CL:0000084 T cell -CL:0000814 mature NK T cell CL:0000913 CD8+ T-cells CD8+ Tem CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell CL:0000913 CD8+ T-cells CD8+ Tem CL:0002419 mature T cell -CL:0000910 cytotoxic T cell CL:0000913 CD8+ T-cells CD8+ Tem CL:0002419 mature T cell -CL:0000912 helper T cell CL:0000913 CD8+ T-cells CD8+ Tem CL:0002419 mature T cell -CL:0000813 memory T cell CL:0000913 CD8+ T-cells CD8+ Tem CL:0000813 memory T cell -CL:0000815 regulatory T cell CL:0000913 CD8+ T-cells CD8+ Tem CL:0002419 mature T cell -CL:0000623 natural killer cell CL:0000623 NK cells NK cells CL:0000623 natural killer cell -CL:0001069 group 2 innate lymphoid cell CL:0000623 NK cells NK cells CL:0001065 innate lymphoid cell -CL:0000236 B cell CL:0000788 B-cells naive B-cells CL:0000236 B cell -CL:0000786 plasma cell CL:0000788 B-cells naive B-cells CL:0000945 lymphocyte of B lineage -CL:0000787 memory B cell CL:0000788 B-cells naive B-cells CL:0000785 mature B cell -CL:0000788 naive B cell CL:0000788 B-cells naive B-cells CL:0000788 naive B cell -CL:0000236 B cell CL:0000787 B-cells Memory B-cells CL:0000236 B cell -CL:0000786 plasma cell CL:0000787 B-cells Memory B-cells CL:0000945 lymphocyte of B lineage -CL:0000787 memory B cell CL:0000787 B-cells Memory B-cells CL:0000787 memory B cell -CL:0000788 naive B cell CL:0000787 B-cells Memory B-cells CL:0000785 mature B cell -CL:0000236 B cell CL:0000972 B-cells Class-switched memory B-cells CL:0000236 B cell -CL:0000786 plasma cell CL:0000972 B-cells Class-switched memory B-cells CL:0000945 lymphocyte of B lineage -CL:0000787 memory B cell CL:0000972 B-cells Class-switched memory B-cells CL:0000787 memory B cell -CL:0000788 naive B cell CL:0000972 B-cells Class-switched memory B-cells CL:0000785 mature B cell -CL:0000646 basal cell CL:0000037 HSC HSC CL:0000723 somatic stem cell -CL:0002322 embryonic stem cell CL:0000037 HSC HSC CL:0000034 stem cell -CL:0000352 epiblast cell CL:0000037 HSC HSC CL:0000723 somatic stem cell -CL:0000037 hematopoietic stem cell CL:0000037 HSC HSC CL:0000037 hematopoietic stem cell -CL:0005026 hepatoblast CL:0000037 HSC HSC CL:0000034 stem cell -CL:0002248 pluripotent stem cell CL:0000037 HSC HSC CL:0000723 somatic stem cell -CL:0002672 retinal progenitor cell CL:0000037 HSC HSC CL:0000034 stem cell -CL:0002664 cardioblast CL:0000037 HSC HSC CL:0000034 stem cell -CL:0002250 intestinal crypt stem cell CL:0000037 HSC HSC CL:0000034 stem cell -CL:0000038 erythroid progenitor cell CL:0000037 HSC HSC CL:0008001 hematopoietic precursor cell -CL:0000324 metanephric mesenchyme stem cell CL:0000037 HSC HSC CL:0000034 stem cell -CL:0000037 hematopoietic stem cell CL:0000837 HSC MPP CL:0008001 hematopoietic precursor cell -CL:0000038 erythroid progenitor cell CL:0000837 HSC MPP CL:0008001 hematopoietic precursor cell -CL:0000037 hematopoietic stem cell CL:0000051 HSC CLP CL:0008001 hematopoietic precursor cell -CL:0000038 erythroid progenitor cell CL:0000051 HSC CLP CL:0008001 hematopoietic precursor cell -CL:0000037 hematopoietic stem cell CL:0000557 HSC GMP CL:0008001 hematopoietic precursor cell -CL:0000038 erythroid progenitor cell CL:0000557 HSC GMP CL:0008001 hematopoietic precursor cell -CL:0000583 alveolar macrophage CL:0000235 Macrophages Macrophages CL:0000235 macrophage -CL:0000767 basophil CL:0000235 Macrophages Macrophages CL:0000766 myeloid leukocyte -CL:0000771 eosinophil CL:0000235 Macrophages Macrophages CL:0000766 myeloid leukocyte -CL:0000235 macrophage CL:0000235 Macrophages Macrophages CL:0000235 macrophage -CL:0000097 mast cell CL:0000235 Macrophages Macrophages CL:0000766 myeloid leukocyte -CL:0000775 neutrophil CL:0000235 Macrophages Macrophages CL:0000766 myeloid leukocyte -CL:0000091 Kupffer cell CL:0000235 Macrophages Macrophages CL:0000235 macrophage -CL:0000129 microglial cell CL:0000235 Macrophages Macrophages CL:0000235 macrophage -CL:0000889 myeloid suppressor cell CL:0000235 Macrophages Macrophages CL:0000766 myeloid leukocyte -CL:0000874 splenic red pulp macrophage CL:0000235 Macrophages Macrophages CL:0000235 macrophage -CL:0000084 T cell CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000084 T cell -CL:0002038 T follicular helper cell CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000791 mature alpha-beta T cell -CL:0000893 thymocyte CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000084 T cell -CL:0000798 gamma-delta T cell CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000084 T cell -CL:0000814 mature NK T cell CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000791 mature alpha-beta T cell -CL:0000898 naive T cell CL:0000625 CD8+ T-cells CD8+ T-cells CL:0002419 mature T cell -CL:0000910 cytotoxic T cell CL:0000625 CD8+ T-cells CD8+ T-cells CL:0002419 mature T cell -CL:0000912 helper T cell CL:0000625 CD8+ T-cells CD8+ T-cells CL:0002419 mature T cell -CL:0000813 memory T cell CL:0000625 CD8+ T-cells CD8+ T-cells CL:0002419 mature T cell -CL:0000815 regulatory T cell CL:0000625 CD8+ T-cells CD8+ T-cells CL:0002419 mature T cell -CL:0000765 erythroblast CL:0000232 Erythrocytes Erythrocytes CL:0000764 erythroid lineage cell -CL:0000558 reticulocyte CL:0000232 Erythrocytes Erythrocytes CL:0000764 erythroid lineage cell -CL:0000038 erythroid progenitor cell CL:0000232 Erythrocytes Erythrocytes CL:0000764 erythroid lineage cell -CL:0000556 megakaryocyte CL:0000556 HSC Megakaryocytes CL:0000556 megakaryocyte -CL:0000037 hematopoietic stem cell CL:0000049 HSC CMP CL:0008001 hematopoietic precursor cell -CL:0000038 erythroid progenitor cell CL:0000049 HSC CMP CL:0008001 hematopoietic precursor cell -CL:0000583 alveolar macrophage CL:0000863 Macrophages Macrophages M1 CL:0000235 macrophage -CL:0000767 basophil CL:0000863 Macrophages Macrophages M1 CL:0000766 myeloid leukocyte -CL:0000771 eosinophil CL:0000863 Macrophages Macrophages M1 CL:0000766 myeloid leukocyte -CL:0000235 macrophage CL:0000863 Macrophages Macrophages M1 CL:0000235 macrophage -CL:0000097 mast cell CL:0000863 Macrophages Macrophages M1 CL:0000766 myeloid leukocyte -CL:0000775 neutrophil CL:0000863 Macrophages Macrophages M1 CL:0000766 myeloid leukocyte -CL:0000091 Kupffer cell CL:0000863 Macrophages Macrophages M1 CL:0000235 macrophage -CL:0000129 microglial cell CL:0000863 Macrophages Macrophages M1 CL:0000235 macrophage -CL:0000889 myeloid suppressor cell CL:0000863 Macrophages Macrophages M1 CL:0000766 myeloid leukocyte -CL:0000874 splenic red pulp macrophage CL:0000863 Macrophages Macrophages M1 CL:0000235 macrophage -CL:0000583 alveolar macrophage CL:0000890 Macrophages Macrophages M2 CL:0000235 macrophage -CL:0000767 basophil CL:0000890 Macrophages Macrophages M2 CL:0000766 myeloid leukocyte -CL:0000771 eosinophil CL:0000890 Macrophages Macrophages M2 CL:0000766 myeloid leukocyte -CL:0000235 macrophage CL:0000890 Macrophages Macrophages M2 CL:0000235 macrophage -CL:0000097 mast cell CL:0000890 Macrophages Macrophages M2 CL:0000766 myeloid leukocyte -CL:0000775 neutrophil CL:0000890 Macrophages Macrophages M2 CL:0000766 myeloid leukocyte -CL:0000091 Kupffer cell CL:0000890 Macrophages Macrophages M2 CL:0000235 macrophage -CL:0000129 microglial cell CL:0000890 Macrophages Macrophages M2 CL:0000235 macrophage -CL:0000889 myeloid suppressor cell CL:0000890 Macrophages Macrophages M2 CL:0000766 myeloid leukocyte -CL:0000874 splenic red pulp macrophage CL:0000890 Macrophages Macrophages M2 CL:0000235 macrophage -CL:0000115 endothelial cell CL:0000115 Endothelial cells Endothelial cells CL:0000115 endothelial cell -CL:0002544 aortic endothelial cell CL:0000115 Endothelial cells Endothelial cells CL:0000115 endothelial cell -CL:2000044 brain microvascular endothelial cell CL:0000115 Endothelial cells Endothelial cells CL:0000115 endothelial cell -CL:0000451 dendritic cell CL:0000451 DC DC CL:0000451 dendritic cell -CL:0000576 monocyte CL:0000451 DC DC CL:0000113 mononuclear phagocyte -CL:0000784 plasmacytoid dendritic cell CL:0000451 DC DC CL:0000451 dendritic cell -CL:0000453 Langerhans cell CL:0000451 DC DC CL:0000451 dendritic cell -CL:0000583 alveolar macrophage CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000767 basophil CL:0000771 Eosinophils Eosinophils CL:0000094 granulocyte -CL:0000771 eosinophil CL:0000771 Eosinophils Eosinophils CL:0000771 eosinophil -CL:0000235 macrophage CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000097 mast cell CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000576 monocyte CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000775 neutrophil CL:0000771 Eosinophils Eosinophils CL:0000094 granulocyte -CL:0000092 osteoclast CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000091 Kupffer cell CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000453 Langerhans cell CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000129 microglial cell CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000889 myeloid suppressor cell CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000874 splenic red pulp macrophage CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte -CL:0000236 B cell CL:0000786 B-cells Plasma cells CL:0000945 lymphocyte of B lineage -CL:0000786 plasma cell CL:0000786 B-cells Plasma cells CL:0000786 plasma cell -CL:0000787 memory B cell CL:0000786 B-cells Plasma cells CL:0000945 lymphocyte of B lineage -CL:0000788 naive B cell CL:0000786 B-cells Plasma cells CL:0000945 lymphocyte of B lineage -CL:0000138 chondrocyte CL:0000138 Chondrocytes Chondrocytes CL:0000138 chondrocyte -CL:2000002 decidual cell CL:0000138 Chondrocytes Chondrocytes CL:0000499 stromal cell -CL:0000632 hepatic stellate cell CL:0000138 Chondrocytes Chondrocytes CL:0000327 extracellular matrix secreting cell -CL:0000499 stromal cell CL:0000138 Chondrocytes Chondrocytes CL:0000499 stromal cell -CL:0000708 leptomeningeal cell CL:0000138 Chondrocytes Chondrocytes CL:0000327 extracellular matrix secreting cell -CL:0000057 fibroblast CL:0000057 Fibroblasts Fibroblasts CL:0000057 fibroblast -CL:0000632 hepatic stellate cell CL:0000057 Fibroblasts Fibroblasts CL:0000057 fibroblast -CL:0002410 pancreatic stellate cell CL:0000057 Fibroblasts Fibroblasts CL:0000057 fibroblast -CL:0002334 preadipocyte CL:0000057 Fibroblasts Fibroblasts CL:0000057 fibroblast -CL:0000192 smooth muscle cell CL:0000192 Smooth muscle Smooth muscle CL:0000192 smooth muscle cell -CL:0019019 tracheobronchial smooth muscle cell CL:0000192 Smooth muscle Smooth muscle CL:0000192 smooth muscle cell -CL:0000746 cardiac muscle cell CL:0000192 Smooth muscle Smooth muscle CL:0000187 muscle cell -CL:0000359 vascular associated smooth muscle cell CL:0000192 Smooth muscle Smooth muscle CL:0000192 smooth muscle cell -CL:0002068 Purkinje myocyte CL:0000192 Smooth muscle Smooth muscle CL:0000187 muscle cell -CL:0000622 acinar cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:1000488 cholangiocyte CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000166 chromaffin cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000584 enterocyte CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000164 enteroendocrine cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000065 ependymal cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000066 epithelial cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000160 goblet cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000501 granulosa cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000182 hepatocyte CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0005006 ionocyte CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000312 keratinocyte CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000077 mesothelial cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000185 myoepithelial cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000165 neuroendocrine cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002167 olfactory epithelial cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000510 paneth cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000162 parietal cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002481 peritubular myoid cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000652 pinealocyte CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000653 podocyte CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000209 taste receptor cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000731 urothelial cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002368 respiratory epithelial cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002370 respiratory goblet cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000171 pancreatic A cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000169 type B pancreatic cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000706 choroid plexus epithelial cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000158 club cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002250 intestinal crypt stem cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000173 pancreatic D cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002305 epithelial cell of distal tubule CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002079 pancreatic ductal cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000504 enterochromaffin-like cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0005019 pancreatic epsilon cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002258 thyroid follicular cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002179 foveolar cell of stomach CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000696 PP cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000155 peptic cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002292 type I cell of carotid body CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0005010 renal intercalated cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:1000909 kidney loop of Henle epithelial cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002326 luminal epithelial cell of mammary gland CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002327 mammary gland epithelial cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000242 Merkel cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000682 M cell of gut CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002199 oxyphil cell of parathyroid gland CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000446 chief cell of parathyroid gland CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0005009 renal principal cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002306 epithelial cell of proximal tubule CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002062 pulmonary alveolar type 1 cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002063 pulmonary alveolar type 2 cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:1001596 salivary gland glandular cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002140 acinar cell of sebaceous gland CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000216 Sertoli cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002562 hair germinal matrix cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0002204 brush cell CL:0000066 Epithelial cells Epithelial cells CL:0000066 epithelial cell -CL:0000148 melanocyte CL:0000148 Melanocytes Melanocytes CL:0000148 melanocyte -CL:0000594 skeletal muscle satellite cell CL:0000188 Skeletal muscle Skeletal muscle CL:0000188 cell of skeletal muscle -CL:0000166 chromaffin cell CL:0000312 Keratinocytes Keratinocytes CL:0002077 ecto-epithelial cell -CL:0000065 ependymal cell CL:0000312 Keratinocytes Keratinocytes CL:0002077 ecto-epithelial cell -CL:0000312 keratinocyte CL:0000312 Keratinocytes Keratinocytes CL:0000312 keratinocyte -CL:0000077 mesothelial cell CL:0000312 Keratinocytes Keratinocytes CL:0000076 squamous epithelial cell -CL:0000165 neuroendocrine cell CL:0000312 Keratinocytes Keratinocytes CL:0002077 ecto-epithelial cell -CL:0002167 olfactory epithelial cell CL:0000312 Keratinocytes Keratinocytes CL:0002077 ecto-epithelial cell -CL:0002481 peritubular myoid cell CL:0000312 Keratinocytes Keratinocytes CL:0000076 squamous epithelial cell -CL:0000652 pinealocyte CL:0000312 Keratinocytes Keratinocytes CL:0002077 ecto-epithelial cell -CL:0000706 choroid plexus epithelial cell CL:0000312 Keratinocytes Keratinocytes CL:0002077 ecto-epithelial cell -CL:0002292 type I cell of carotid body CL:0000312 Keratinocytes Keratinocytes CL:0002077 ecto-epithelial cell -CL:0000242 Merkel cell CL:0000312 Keratinocytes Keratinocytes CL:0000312 keratinocyte -CL:0002062 pulmonary alveolar type 1 cell CL:0000312 Keratinocytes Keratinocytes CL:0000076 squamous epithelial cell -CL:0002063 pulmonary alveolar type 2 cell CL:0000312 Keratinocytes Keratinocytes CL:0000076 squamous epithelial cell -CL:0002140 acinar cell of sebaceous gland CL:0000312 Keratinocytes Keratinocytes CL:0000362 epidermal cell -CL:0000216 Sertoli cell CL:0000312 Keratinocytes Keratinocytes CL:0000076 squamous epithelial cell -CL:0002562 hair germinal matrix cell CL:0000312 Keratinocytes Keratinocytes CL:0000362 epidermal cell -CL:0000115 endothelial cell CL:2000008 Endothelial cells mv Endothelial cells CL:0000115 endothelial cell -CL:0002544 aortic endothelial cell CL:2000008 Endothelial cells mv Endothelial cells CL:0000071 blood vessel endothelial cell -CL:2000044 brain microvascular endothelial cell CL:2000008 Endothelial cells mv Endothelial cells CL:2000008 microvascular endothelial cell -CL:0000192 smooth muscle cell CL:0000187 Myocytes Myocytes CL:0000187 muscle cell -CL:0019019 tracheobronchial smooth muscle cell CL:0000187 Myocytes Myocytes CL:0000187 muscle cell -CL:0000746 cardiac muscle cell CL:0000187 Myocytes Myocytes CL:0000187 muscle cell -CL:0000359 vascular associated smooth muscle cell CL:0000187 Myocytes Myocytes CL:0000187 muscle cell -CL:0002068 Purkinje myocyte CL:0000187 Myocytes Myocytes CL:0000187 muscle cell -CL:0000136 adipocyte CL:0000136 Adipocytes Adipocytes CL:0000136 adipocyte -CL:0000650 mesangial cell CL:0000669 Pericytes Pericytes CL:0000669 pericyte -CL:0000669 pericyte CL:0000669 Pericytes Pericytes CL:0000669 pericyte -CL:0000127 astrocyte CL:0000127 Astrocytes Astrocytes CL:0000127 astrocyte -CL:0000065 ependymal cell CL:0000127 Astrocytes Astrocytes CL:0000125 glial cell -CL:0000128 oligodendrocyte CL:0000127 Astrocytes Astrocytes CL:0000126 macroglial cell -CL:0002085 tanycyte CL:0000127 Astrocytes Astrocytes CL:0000127 astrocyte -CL:0000644 Bergmann glial cell CL:0000127 Astrocytes Astrocytes CL:0000127 astrocyte -CL:0000706 choroid plexus epithelial cell CL:0000127 Astrocytes Astrocytes CL:0000125 glial cell -CL:4040002 enteroglial cell CL:0000127 Astrocytes Astrocytes CL:0000125 glial cell -CL:4042021 neuronal-restricted precursor CL:0000127 Astrocytes Astrocytes CL:0000095 neuron associated cell -CL:0000242 Merkel cell CL:0000127 Astrocytes Astrocytes CL:0000095 neuron associated cell -CL:0000129 microglial cell CL:0000127 Astrocytes Astrocytes CL:0000125 glial cell -CL:0000636 Mueller cell CL:0000127 Astrocytes Astrocytes CL:0000125 glial cell -CL:0002453 oligodendrocyte precursor cell CL:0000127 Astrocytes Astrocytes CL:0000095 neuron associated cell -CL:0002573 Schwann cell CL:0000127 Astrocytes Astrocytes CL:0000125 glial cell -CL:0000681 radial glial cell CL:0000127 Astrocytes Astrocytes CL:0000125 glial cell -CL:0000516 perineural satellite cell CL:0000127 Astrocytes Astrocytes CL:0000095 neuron associated cell -CL:0000650 mesangial cell CL:0000650 Mesangial cells Mesangial cells CL:0000650 mesangial cell -CL:0000669 pericyte CL:0000650 Mesangial cells Mesangial cells CL:0000669 pericyte +panglao_ontology panglao_annotation original_panglao_name blueprint_ontology blueprint_annotation_main blueprint_annotation_fine consensus_ontology consensus_annotation +CL:0000583 alveolar macrophage Alveolar macrophages CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte +CL:0000767 basophil Basophils CL:0000775 Neutrophils Neutrophils CL:0000094 granulocyte +CL:0000771 eosinophil Eosinophils CL:0000775 Neutrophils Neutrophils CL:0000094 granulocyte +CL:0000235 macrophage Macrophages CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte +CL:0000097 mast cell Mast cells CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte +CL:0000576 monocyte Monocytes CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte +CL:0000576 monocyte Osteoclast precursor cells CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte +CL:0000775 neutrophil Neutrophils CL:0000775 Neutrophils Neutrophils CL:0000775 neutrophil +CL:0000092 osteoclast Osteoclasts CL:0000775 Neutrophils Neutrophils CL:0000766 myeloid leukocyte +CL:0000091 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CD4+ T-cells CD4+ Tem CL:0000624 CD4-positive, alpha-beta T cell +CL:0000893 thymocyte Thymocytes CL:0000905 CD4+ T-cells CD4+ Tem CL:0000084 T cell +CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0000084 T cell +CL:0000814 mature NK T cell Natural killer T cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0000791 mature alpha-beta T cell +CL:0000898 naive T cell T cells naive CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell +CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell +CL:0000912 helper T cell T helper cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell +CL:0000813 memory T cell T memory cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0000813 memory T cell +CL:0000815 regulatory T cell T regulatory cells CL:0000905 CD4+ T-cells CD4+ Tem CL:0002419 mature T cell +CL:0000084 T cell T cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000084 T cell +CL:0002038 T follicular helper cell T follicular helper cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000791 mature alpha-beta T cell +CL:0000893 thymocyte Thymocytes CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000084 T cell +CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000084 T cell +CL:0000814 mature NK T cell Natural killer T cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000791 mature alpha-beta T cell +CL:0000898 naive T cell T cells naive CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell +CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell +CL:0000912 helper T cell T helper cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell +CL:0000813 memory T cell T memory cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0000813 memory T cell +CL:0000815 regulatory T cell T regulatory cells CL:0000907 CD8+ T-cells CD8+ Tcm CL:0002419 mature T cell +CL:0000084 T cell T cells CL:0000913 CD8+ T-cells CD8+ Tem CL:0000084 T cell +CL:0002038 T 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cell +CL:0000786 plasma cell Plasma cells CL:0000972 B-cells Class-switched memory B-cells CL:0000945 lymphocyte of B lineage +CL:0000787 memory B cell B cells memory CL:0000972 B-cells Class-switched memory B-cells CL:0000787 memory B cell +CL:0000788 naive B cell B cells naive CL:0000972 B-cells Class-switched memory B-cells CL:0000785 mature B cell +CL:0000646 basal cell Basal cells CL:0000037 HSC HSC CL:0000723 somatic stem cell +CL:0002322 embryonic stem cell Embryonic stem cells CL:0000037 HSC HSC CL:0000034 stem cell +CL:0000352 epiblast cell Epiblast cells CL:0000037 HSC HSC CL:0000723 somatic stem cell +CL:0000037 hematopoietic stem cell Hematopoietic stem cells CL:0000037 HSC HSC CL:0000037 hematopoietic stem cell +CL:0005026 hepatoblast Hepatoblasts CL:0000037 HSC HSC CL:0000034 stem cell +CL:0002248 pluripotent stem cell Pluripotent stem cells CL:0000037 HSC HSC CL:0000723 somatic stem cell +CL:0002672 retinal progenitor cell Retinal progenitor cells CL:0000037 HSC HSC 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Macrophages CL:0000235 macrophage +CL:0000889 myeloid suppressor cell Myeloid-derived suppressor cells CL:0000235 Macrophages Macrophages CL:0000766 myeloid leukocyte +CL:0000874 splenic red pulp macrophage Red pulp macrophages CL:0000235 Macrophages Macrophages CL:0000235 macrophage +CL:0000084 T cell T cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000084 T cell +CL:0002038 T follicular helper cell T follicular helper cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000791 mature alpha-beta T cell +CL:0000893 thymocyte Thymocytes CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000084 T cell +CL:0000798 gamma-delta T cell Gamma delta T cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000084 T cell +CL:0000814 mature NK T cell Natural killer T cells CL:0000625 CD8+ T-cells CD8+ T-cells CL:0000791 mature alpha-beta T cell +CL:0000898 naive T cell T cells naive CL:0000625 CD8+ T-cells CD8+ T-cells CL:0002419 mature T cell +CL:0000910 cytotoxic T cell T cytotoxic cells CL:0000625 CD8+ T-cells CD8+ 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Myeloid-derived suppressor cells CL:0000890 Macrophages Macrophages M2 CL:0000766 myeloid leukocyte +CL:0000874 splenic red pulp macrophage Red pulp macrophages CL:0000890 Macrophages Macrophages M2 CL:0000235 macrophage +CL:0000115 endothelial cell Endothelial cells CL:0000115 Endothelial cells Endothelial cells CL:0000115 endothelial cell +CL:0002544 aortic endothelial cell Endothelial cells (aorta) CL:0000115 Endothelial cells Endothelial cells CL:0000115 endothelial cell +CL:2000044 brain microvascular endothelial cell Endothelial cells (blood brain barrier) CL:0000115 Endothelial cells Endothelial cells CL:0000115 endothelial cell +CL:0000451 dendritic cell Dendritic cells CL:0000451 DC DC CL:0000451 dendritic cell +CL:0000576 monocyte Monocytes CL:0000451 DC DC CL:0000113 mononuclear phagocyte +CL:0000576 monocyte Osteoclast precursor cells CL:0000451 DC DC CL:0000113 mononuclear phagocyte +CL:0000784 plasmacytoid dendritic cell Plasmacytoid dendritic cells CL:0000451 DC DC CL:0000451 dendritic cell +CL:0000453 Langerhans cell Langerhans cells CL:0000451 DC DC CL:0000451 dendritic cell +CL:0000583 alveolar macrophage Alveolar macrophages CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte +CL:0000767 basophil Basophils CL:0000771 Eosinophils Eosinophils CL:0000094 granulocyte +CL:0000771 eosinophil Eosinophils CL:0000771 Eosinophils Eosinophils CL:0000771 eosinophil +CL:0000235 macrophage Macrophages CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte +CL:0000097 mast cell Mast cells CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte +CL:0000576 monocyte Monocytes CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte +CL:0000576 monocyte Osteoclast precursor cells CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid leukocyte +CL:0000775 neutrophil Neutrophils CL:0000771 Eosinophils Eosinophils CL:0000094 granulocyte +CL:0000092 osteoclast Osteoclasts CL:0000771 Eosinophils Eosinophils CL:0000766 myeloid 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cells CL:0000127 Astrocytes Astrocytes CL:0000125 glial cell +CL:0000681 radial glial cell Radial glia cells CL:0000127 Astrocytes Astrocytes CL:0000125 glial cell +CL:0000516 perineural satellite cell Satellite glial cells CL:0000127 Astrocytes Astrocytes CL:0000095 neuron associated cell +CL:0000650 mesangial cell Mesangial cells CL:0000650 Mesangial cells Mesangial cells CL:0000650 mesangial cell +CL:0000669 pericyte Pericytes CL:0000650 Mesangial cells Mesangial cells CL:0000669 pericyte diff --git a/analyses/cell-type-consensus/scripts/02-prepare-consensus-reference.R b/analyses/cell-type-consensus/scripts/02-prepare-consensus-reference.R index 4171ed363..3915685a0 100644 --- a/analyses/cell-type-consensus/scripts/02-prepare-consensus-reference.R +++ b/analyses/cell-type-consensus/scripts/02-prepare-consensus-reference.R @@ -27,10 +27,11 @@ panglao_df <- readr::read_tsv(panglao_ref_file) |> # rename columns to have panglao in them for easy joining later dplyr::select( panglao_ontology = "ontology_id", - panglao_annotation = "human_readable_value" + panglao_annotation = "human_readable_value", + original_panglao_name = "panglao_cell_type" # keep original name since some map to the same ontology ID ) |> # remove any cell types that don't have ontologies - tidyr::drop_na() + tidyr::drop_na() # grab singler ref from celldex blueprint_ref <- celldex::BlueprintEncodeData() @@ -116,6 +117,7 @@ consensus_labels_df <- lca_df |> dplyr::select( panglao_ontology, panglao_annotation, + original_panglao_name, blueprint_ontology, blueprint_annotation_main, blueprint_annotation_fine,