spatialcore 0.1.9__py3-none-any.whl

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Files changed (36) hide show
  1. spatialcore/__init__.py +122 -0
  2. spatialcore/annotation/__init__.py +253 -0
  3. spatialcore/annotation/acquisition.py +529 -0
  4. spatialcore/annotation/annotate.py +603 -0
  5. spatialcore/annotation/cellxgene.py +365 -0
  6. spatialcore/annotation/confidence.py +802 -0
  7. spatialcore/annotation/discovery.py +529 -0
  8. spatialcore/annotation/expression.py +363 -0
  9. spatialcore/annotation/loading.py +529 -0
  10. spatialcore/annotation/markers.py +297 -0
  11. spatialcore/annotation/ontology.py +1282 -0
  12. spatialcore/annotation/patterns.py +247 -0
  13. spatialcore/annotation/pipeline.py +620 -0
  14. spatialcore/annotation/synapse.py +380 -0
  15. spatialcore/annotation/training.py +1457 -0
  16. spatialcore/annotation/validation.py +422 -0
  17. spatialcore/core/__init__.py +34 -0
  18. spatialcore/core/cache.py +118 -0
  19. spatialcore/core/logging.py +135 -0
  20. spatialcore/core/metadata.py +149 -0
  21. spatialcore/core/utils.py +768 -0
  22. spatialcore/data/gene_mappings/ensembl_to_hugo_human.tsv +86372 -0
  23. spatialcore/data/markers/canonical_markers.json +83 -0
  24. spatialcore/data/ontology_mappings/ontology_index.json +63865 -0
  25. spatialcore/plotting/__init__.py +109 -0
  26. spatialcore/plotting/benchmark.py +477 -0
  27. spatialcore/plotting/celltype.py +329 -0
  28. spatialcore/plotting/confidence.py +413 -0
  29. spatialcore/plotting/spatial.py +505 -0
  30. spatialcore/plotting/utils.py +411 -0
  31. spatialcore/plotting/validation.py +1342 -0
  32. spatialcore-0.1.9.dist-info/METADATA +213 -0
  33. spatialcore-0.1.9.dist-info/RECORD +36 -0
  34. spatialcore-0.1.9.dist-info/WHEEL +5 -0
  35. spatialcore-0.1.9.dist-info/licenses/LICENSE +201 -0
  36. spatialcore-0.1.9.dist-info/top_level.txt +1 -0
spatialcore/data/markers/canonical_markers.json ADDED
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+ {
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+ "metadata": {
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+ "description": "Canonical cell type markers for spatial transcriptomics analysis",
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+ "source": "Derived from hieratype_markers.json index markers plus established literature markers",
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+ "cell_types_from": "Cell Ontology (CL) via ontology_index.json - keys are lowercase for case-insensitive lookup",
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+ "version": "1.2.0",
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+ "changelog": "v1.2.0: Merged 24 additional cell types from markers.py hardcoded dict (myofibroblast, memory T cell, etc.)"
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+ },
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+ "markers": {
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+ "epithelial cell": ["EPCAM", "KRT18", "KRT19", "CDH1", "KRT8", "KRT7", "CLDN4"],
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+ "endothelial cell": ["PECAM1", "VWF", "CDH5", "CLDN5", "ENG", "FLT1", "KDR", "CD34"],
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+ "fibroblast": ["COL1A1", "DCN", "PDGFRA", "COL1A2", "VIM", "LUM", "FAP", "THY1"],
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+ "smooth muscle cell": ["MYH11", "ACTA2", "TAGLN", "DES", "CNN1", "MYLK", "MYL9", "CALD1"],
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+ "plasma cell": ["IGHG1", "IGHA1", "MZB1", "JCHAIN", "SDC1", "PRDM1", "XBP1", "CD38"],
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+ "t cell": ["CD3D", "CD3G", "CD3E", "IL7R", "TRBC1", "CD2", "TCF7", "LEF1"],
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+ "cd4-positive, alpha-beta t cell": ["CD4", "IL7R", "CD40LG", "FOXP3", "IL2RA"],
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+ "cd8-positive, alpha-beta t cell": ["CD8A", "CD8B", "GZMK", "GZMA", "PRF1", "EOMES"],
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+ "b cell": ["CD19", "MS4A1", "CD79A", "CD79B", "PAX5", "CD22", "BANK1", "BLK"],
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+ "macrophage": ["CD163", "CD68", "MARCO", "CSF1R", "MERTK", "C1QA", "C1QB", "C1QC", "MRC1"],
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+ "alveolar macrophage": ["MARCO", "FABP4", "MCEMP1", "PPARG", "CD163", "CD68", "SIGLEC1", "MRC1"],
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+ "monocyte": ["CD14", "FCGR3A", "CCR2", "LYZ", "S100A8", "S100A9", "VCAN", "FCN1"],
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+ "dendritic cell": ["ITGAX", "CLEC9A", "FLT3", "XCR1", "CD1C", "IRF8", "BATF3", "CCR7"],
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+ "plasmacytoid dendritic cell": ["IL3RA", "CLEC4C", "TCF4", "IRF7", "LILRA4", "GZMB"],
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+ "natural killer cell": ["GNLY", "KLRD1", "KLRF1", "NKG7", "FCGR3A", "NCAM1", "NCR1", "KLRK1"],
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+ "neutrophil": ["MPO", "FCGR3B", "S100A8", "S100A9", "CSF3R", "CXCR2", "ELANE", "CEACAM8"],
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+ "mast cell": ["KIT", "TPSAB1", "TPSB2", "CPA3", "HDC", "FCER1A", "MS4A2", "GATA2"],
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+ "eosinophil": ["CLC", "PRG2", "SIGLEC8", "EPX", "JAML", "CCR3", "IL5RA", "RNASE2"],
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+ "basophil": ["CLC", "GATA2", "HDC", "IL3RA", "FCER1A"],
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+ "hepatocyte": ["ALB", "APOB", "CYP3A4", "HNF4A", "CYP2E1", "PCK1", "G6PC", "TAT"],
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+ "cholangiocyte": ["KRT19", "KRT7", "EPCAM", "SOX9", "CFTR", "AQP1", "CLDN4"],
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+ "cardiac muscle cell": ["TNNT2", "MYH7", "MYH6", "ACTC1", "TTN", "RYR2", "MYBPC3"],
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+ "neuron": ["RBFOX3", "SYN1", "MAP2", "TUBB3", "SNAP25", "SYP", "NEFL", "ENO2"],
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+ "astrocyte": ["GFAP", "AQP4", "S100B", "SLC1A3", "ALDH1L1", "GJA1", "SLC1A2"],
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+ "oligodendrocyte": ["MBP", "MOG", "PLP1", "OLIG2", "MAG", "CNP", "CLDN11"],
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+ "microglial cell": ["CX3CR1", "P2RY12", "TMEM119", "ITGAM", "AIF1", "CSF1R", "HEXB", "TREM2"],
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+ "adipocyte": ["ADIPOQ", "LEP", "FABP4", "PPARG", "PLIN1", "LPL", "CFD", "CIDEC"],
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+ "pericyte": ["PDGFRB", "RGS5", "KCNJ8", "ABCC9", "NOTCH3", "CSPG4", "DES"],
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+ "schwann cell": ["MPZ", "PMP22", "S100B", "SOX10", "EGR2", "MBP", "PRX"],
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+ "enterocyte": ["FABP2", "SLC5A1", "APOA1", "ALPI", "SI", "VIL1", "RBP2"],
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+ "goblet cell": ["MUC2", "TFF3", "CLCA1", "SPINK4", "FCGBP", "ZG16", "AGR2"],
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+ "paneth cell": ["DEFA5", "DEFA6", "LYZ", "REG3A", "MMP7", "CA7"],
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+ "tuft cell": ["DCLK1", "TRPM5", "POU2F3", "GFI1B", "LRMP", "SH2D6", "AVIL"],
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+ "intestinal tuft cell": ["DCLK1", "TRPM5", "POU2F3", "GFI1B", "LRMP", "SH2D6", "AVIL"],
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+ "enteroendocrine cell": ["CHGA", "CHGB", "SYP", "NEUROD1", "GCG", "PYY", "CCK", "GIP"],
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+ "type i pneumocyte": ["AGER", "PDPN", "HOPX", "CAV1", "AQP5", "CLIC5", "EMP2"],
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+ "type ii pneumocyte": ["SFTPC", "SFTPB", "SFTPA1", "ABCA3", "LAMP3", "NKX2-1", "NAPSA"],
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+ "club cell": ["SCGB1A1", "SCGB3A2", "CYP2F1", "BPIFA1", "KRT15"],
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+ "ciliated cell": ["FOXJ1", "TPPP3", "PIFO", "CAPS", "DNAH5", "CFAP43", "SPAG17"],
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+ "basal cell": ["KRT5", "KRT14", "TP63", "ITGA6", "ITGB4", "NGFR"],
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+ "mesothelial cell": ["MSLN", "WT1", "UPK3B", "CALB2", "KRT19", "LRRN4"],
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+ "melanocyte": ["MLANA", "PMEL", "TYR", "MITF", "DCT", "TYRP1", "SOX10"],
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+ "keratinocyte": ["KRT1", "KRT10", "KRT14", "IVL", "LOR", "FLG", "DSG1"],
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+ "osteoblast": ["BGLAP", "RUNX2", "SP7", "ALPL", "COL1A1", "IBSP", "SPP1"],
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+ "osteoclast": ["ACP5", "CTSK", "MMP9", "OSCAR", "DCSTAMP", "ATP6V0D2", "TNFRSF11A"],
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+ "chondrocyte": ["COL2A1", "ACAN", "SOX9", "COMP", "COL9A1", "COL11A1", "MATN3"],
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+ "podocyte": ["NPHS1", "NPHS2", "WT1", "PODXL", "SYNPO", "PTPRO", "VEGFA"],
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+ "epithelial cell of proximal tubule": ["LRP2", "SLC34A1", "CUBN", "SLC5A2", "ACSM2A", "SLC22A6"],
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+ "epithelial cell of distal tubule": ["SLC12A3", "CALB1", "TRPV5", "UMOD", "SLC12A1"],
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+ "kidney collecting duct cell": ["AQP2", "FXYD4", "HSD11B2", "SLC4A1", "ATP6V1B1"],
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+ "stromal cell": ["DCN", "LUM", "COL1A1", "COL1A2", "PDGFRA", "FAP", "VIM", "THY1"],
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+ "classical monocyte": ["CD14", "LYZ", "S100A8", "S100A9", "VCAN", "FCN1", "CD36", "CCR2"],
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+ "regulatory t cell": ["FOXP3", "IL2RA", "CTLA4", "TNFRSF18", "IKZF2", "CCR8", "IL7R", "CD4"],
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+
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+ "_comment_additional": "Additional cell types merged from markers.py hardcoded dict",
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+
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+ "gamma-delta t cell": ["TRGC1", "TRGC2", "TRDC", "CD3E"],
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+ "naive t cell": ["CD3E", "CCR7", "SELL", "LEF1", "TCF7"],
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+ "memory t cell": ["CD3E", "CD44", "IL7R", "S100A4"],
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+ "effector t cell": ["CD3E", "GZMB", "PRF1", "IFNG", "NKG7"],
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+ "naive b cell": ["MS4A1", "CD19", "IGHD", "TCL1A", "FCER2"],
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+ "memory b cell": ["MS4A1", "CD27", "IGHG1", "CD19", "AIM2"],
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+ "plasmablast": ["MZB1", "SDC1", "XBP1", "MKI67", "PRDM1"],
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+ "non-classical monocyte": ["FCGR3A", "CDKN1C", "MS4A7", "CX3CR1", "LILRB2"],
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+ "conventional dendritic cell": ["CLEC9A", "XCR1", "CD1C", "BATF3", "IRF8"],
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+ "myofibroblast cell": ["ACTA2", "COL1A1", "COL3A1", "TAGLN", "FAP", "POSTN", "VIM"],
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+ "pneumocyte": ["SFTPC", "SFTPB", "AGER", "HOPX"],
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+ "erythrocyte": ["HBA1", "HBA2", "HBB", "GYPA", "ALAS2"],
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+ "platelet": ["PPBP", "PF4", "GP1BA", "ITGA2B", "SELP"],
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+ "megakaryocyte": ["PPBP", "PF4", "ITGA2B", "GP1BA", "VWF"],
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+ "hepatic stellate cell": ["ACTA2", "COL1A1", "DES", "RGS5", "LRAT"],
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+ "kupffer cell": ["CD68", "CD163", "MARCO", "TIMD4", "CLEC4F"]
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+ }
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+ }