ouroboros 0.9.0__py3-none-any.whl

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Files changed (37) hide show
  1. ouroboros/__init__.py +22 -0
  2. ouroboros/data/SHAP_feature_set.csv +227 -0
  3. ouroboros/data/__init__.py +0 -0
  4. ouroboros/data/all_genes_mouse_orthologs.csv +19147 -0
  5. ouroboros/data/gene_order.csv +227 -0
  6. ouroboros/data/model/__init__.py +0 -0
  7. ouroboros/data/model/model.data-00000-of-00001 +0 -0
  8. ouroboros/data/model/model.index +0 -0
  9. ouroboros/data/model/model.meta +0 -0
  10. ouroboros/data/neurogen_example.h5ad +0 -0
  11. ouroboros/data/reference_embeddings.csv +5699 -0
  12. ouroboros/data/train_matrix.csv +5699 -0
  13. ouroboros/data/train_meta.csv +5699 -0
  14. ouroboros/main.py +263 -0
  15. ouroboros/ouroboros_functions.py +2081 -0
  16. ouroboros/scphere/__init__.py +0 -0
  17. ouroboros/scphere/distributions/__init__.py +3 -0
  18. ouroboros/scphere/distributions/hyperbolic_wrapped_norm.py +201 -0
  19. ouroboros/scphere/distributions/hyperspherical_uniform.py +108 -0
  20. ouroboros/scphere/distributions/von_mises_fisher.py +263 -0
  21. ouroboros/scphere/model/__init__.py +0 -0
  22. ouroboros/scphere/model/vae.py +317 -0
  23. ouroboros/scphere/model/vae_sp.py +390 -0
  24. ouroboros/scphere/ops/__init__.py +1 -0
  25. ouroboros/scphere/ops/ive.py +29 -0
  26. ouroboros/scphere/util/__init__.py +1 -0
  27. ouroboros/scphere/util/data.py +102 -0
  28. ouroboros/scphere/util/plot.py +32 -0
  29. ouroboros/scphere/util/trainer.py +55 -0
  30. ouroboros/scphere/util/trainer_sp.py +55 -0
  31. ouroboros/scphere/util/util.py +61 -0
  32. ouroboros-0.9.0.dist-info/METADATA +121 -0
  33. ouroboros-0.9.0.dist-info/RECORD +37 -0
  34. ouroboros-0.9.0.dist-info/WHEEL +5 -0
  35. ouroboros-0.9.0.dist-info/entry_points.txt +2 -0
  36. ouroboros-0.9.0.dist-info/licenses/LICENSE +21 -0
  37. ouroboros-0.9.0.dist-info/top_level.txt +1 -0
ouroboros/__init__.py ADDED
@@ -0,0 +1,22 @@
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+ import os
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+ os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
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+
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+ import warnings
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+ warnings.filterwarnings("ignore", category=FutureWarning)
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+ warnings.filterwarnings("ignore", category=DeprecationWarning)
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+
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+ from .main import run_ouroboros
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+ from .ouroboros_functions import (
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+ plot_sphere,
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+ check_genes,
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+ read_in_features,
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+ read_in_refembed,
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+ plot_gene_sphere,
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+ find_cycle_pole,
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+ sphere_snapshot,
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+ rotate_north,
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+ convert_to_human_genes,
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+ plot_robinson_projection
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+ )
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+
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+ __version__ = "0.1.0"
ouroboros/data/SHAP_feature_set.csv ADDED
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+ feature_set
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+ BUB1
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+ H1-3
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+ KIF4A
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+ SNCG
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+ AURKB
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+ YPEL3
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+ HMMR
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+ ECT2
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+ CENPF
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+ SPON2
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+ ZNF469
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+ SH3RF2
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+ IL17RE
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+ PTGS1
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+ H4C8
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+ RHOV
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+ IGFBP5
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+ TTK
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+ CDC6
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+ ASPM
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+ CXCL12
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+ CXXC4
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+ F10
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+ CLTRN
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+ MKI67
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+ MCM4
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+ KIF20A
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+ BUB1B
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+ PSMC3IP
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+ VCAN
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+ CKAP2L
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+ CLIP3
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+ CCNE1
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+ CCNB2
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+ ISL1
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+ NUF2
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+ KPNA2
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+ KIF20B
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+ SGO1
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+ WDR76
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+ PYY
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+ GTSE1
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+ ABCC3
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+ CCNB1
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+ UNG
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+ RACGAP1
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+ UGT8
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+ SGO2
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+ CIT
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+ CDC25C
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+ PLD4
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+ E2F8
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+ POLD3
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+ LRRC4C
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+ MEIS1
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+ H1-5
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+ PCDH18
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+ H1-1
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+ MASP1
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+ TOP2A
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+ KIF18B
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+ RAD51
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+ PHLDA1
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+ COL3A1
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+ DTL
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+ PAQR4
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+ SGIP1
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+ MAFB
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+ PPP1R14A
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+ RGCC
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+ CD24
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+ EXO1
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+ HJURP
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+ IQGAP3
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+ SLC22A18
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+ SOX6
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+ RAPSN
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+ PDGFRB
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+ NCAPH
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+ CDCA3
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+ ZNF367
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+ IGF2
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+ HEPACAM2
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+ HMGB2
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+ CDK1
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+ ANKRD1
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+ SYNE2
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+ WNT5B
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+ DSN1
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+ TSPAN7
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+ ACTA2
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+ FAM111A
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+ BRCA1
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+ MCM6
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+ GHRL
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+ DIAPH3
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+ CCNE2
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+ TCF19
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+ H2AC20
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+ CENPA
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+ PIMREG
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+ CDKN1C
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+ SERPING1
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+ GINS2
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+ VWA5B2
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+ UBE2S
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+ NEK2
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+ KIF23
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+ APOE
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+ GAS2L3
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+ INCENP
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+ ATAD2
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+ KLF6
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+ MCM3
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+ MCM5
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+ ARL6IP1
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+ SPON1
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+ MXD4
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+ KIF18A
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+ PCNA
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+ PCSK1
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+ LUM
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+ TPX2
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+ GSN
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+ POLA2
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+ BLM
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+ NRARP
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+ UBE2C
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+ FLRT1
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+ RRM2
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+ SULF1
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+ WDHD1
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+ TNFRSF11B
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+ MCM2
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+ KIF11
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+ RAB27B
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+ NUSAP1
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+ MCM10
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+ KRT17
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+ CDCA7
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+ ARID5B
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+ KIF14
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+ SYTL4
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+ OSBPL6
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+ L1CAM
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+ ERCC6L
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+ STIL
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+ VILL
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+ PDCD4
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+ NDC80
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+ SHF
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+ NEUROD2
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+ VAMP5
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+ NEURL1B
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+ ORC1
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+ MMS22L
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+ CHAF1A
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+ KIF2C
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+ DLGAP5
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+ YPEL2
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+ CLDN9
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+ MELK
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+ TICRR
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+ CLSPN
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+ CENPE
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+ TROAP
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+ DNMT3B
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+ NR5A2
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+ KNSTRN
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+ PLK1
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+ CRYBA2
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+ CDC45
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+ FAM83D
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+ CMTM8
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+ AURKA
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+ CDC20
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+ E2F1
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+ CLDN7
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+ PALMD
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+ CLDN6
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+ NECAB2
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+ FAM43A
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+ H1-4
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+ CHGB
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+ CKAP2
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+ SPRY1
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+ MFSD3
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+ KIAA0040
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+ CEP55
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+ DEPDC1
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+ FBXO5
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+ CDCA8
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+ HYLS1
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+ AMBP
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+ FCGRT
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+ H2BC11
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+ BCL2L14
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+ PIF1
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+ KNL1
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+ FGFR3
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+ SAPCD2
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+ ARRDC3
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+ HELLS
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+ HOXB5
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+ ENHO
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+ TRPV2
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+ UBALD2
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+ FEN1
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+ CDCA2
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+ BRIP1
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+ ESCO2
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+ RFC4
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+ PIGW
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+ SLFN11
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+ CCNF
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+ PSRC1
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+ IRAG1
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+ PLCXD3
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+ CCNA2
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+ TONSL
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+ DHRS13
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+ SPAG5
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+ MGARP
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+ SLBP
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+ PCSK1N
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+ CDKN2D
ouroboros/data/__init__.py ADDED
File without changes