py-CellCall 0.1.0__py3-none-any.whl

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Files changed (37) hide show
  1. cellcall/__init__.py +28 -0
  2. cellcall/connect_profile.py +694 -0
  3. cellcall/correlation.py +93 -0
  4. cellcall/distance.py +72 -0
  5. cellcall/extdata/KEGG_SYMBOL_ID.txt +336 -0
  6. cellcall/extdata/example_Data.Rdata +0 -0
  7. cellcall/extdata/homo/exon_sum.Rdata +0 -0
  8. cellcall/extdata/homo/transcriptmaxLength.Rdata +0 -0
  9. cellcall/extdata/mmus/exon_sum.Rdata +0 -0
  10. cellcall/extdata/mmus/transcriptmaxLength.Rdata +0 -0
  11. cellcall/extdata/new_ligand_receptor_TFs.txt +19145 -0
  12. cellcall/extdata/new_ligand_receptor_TFs_extended.txt +3976 -0
  13. cellcall/extdata/new_ligand_receptor_TFs_homology.txt +12070 -0
  14. cellcall/extdata/new_ligand_receptor_TFs_homology_extended.txt +3458 -0
  15. cellcall/extdata/r_regulons_cache.csv +379 -0
  16. cellcall/extdata/tf_target.txt +591016 -0
  17. cellcall/extdata/tf_target_homology.txt +620618 -0
  18. cellcall/fgsea.py +207 -0
  19. cellcall/fgsea_c.py +85 -0
  20. cellcall/fgsea_numba.py +205 -0
  21. cellcall/foldchange.py +55 -0
  22. cellcall/gsea.py +289 -0
  23. cellcall/gsea_r.py +135 -0
  24. cellcall/io.py +75 -0
  25. cellcall/lr2tf.py +156 -0
  26. cellcall/normalize.py +106 -0
  27. cellcall/object.py +34 -0
  28. cellcall/pathway.py +197 -0
  29. cellcall/rng_compat.py +95 -0
  30. cellcall/src/fgsea_exact.c +212 -0
  31. cellcall/src/fgsea_exact.so +0 -0
  32. cellcall/triple_score.py +43 -0
  33. cellcall/visualization.py +175 -0
  34. py_cellcall-0.1.0.dist-info/METADATA +145 -0
  35. py_cellcall-0.1.0.dist-info/RECORD +37 -0
  36. py_cellcall-0.1.0.dist-info/WHEEL +4 -0
  37. py_cellcall-0.1.0.dist-info/licenses/LICENSE +16 -0
cellcall/__init__.py ADDED
@@ -0,0 +1,28 @@
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+ """
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+ pycellcall - Python port of cellcall: inference of intercellular networks
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+ from single-cell transcriptomics.
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+ """
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+
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+ from .object import CellInter
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+ from .normalize import counts2normalized_10x, counts2normalized_smartseq2
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+ from .connect_profile import connect_profile, trans_commu_profile
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+ from .lr2tf import lr2tf
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+ from .pathway import get_hyper_pathway
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+ from .triple_score import trans2triple_score
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+ from .visualization import plot_bubble, view_pheatmap, get_for_bubble
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+
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+ __version__ = "0.1.0"
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+
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+ __all__ = [
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+ "CellInter",
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+ "counts2normalized_10x",
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+ "counts2normalized_smartseq2",
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+ "connect_profile",
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+ "trans_commu_profile",
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+ "lr2tf",
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+ "get_hyper_pathway",
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+ "trans2triple_score",
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+ "plot_bubble",
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+ "view_pheatmap",
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+ "get_for_bubble",
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+ ]