cpgtools 2.0.0__py3-none-any.whl → 2.0.2__py3-none-any.whl

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Files changed (94) hide show
  1. cpgmodule/_version.py +1 -0
  2. cpgmodule/utils.py +35 -0
  3. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/CpG_aggregation.py +1 -1
  4. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/CpG_anno_position.py +1 -1
  5. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/CpG_anno_probe.py +1 -2
  6. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/CpG_density_gene_centered.py +1 -1
  7. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/CpG_distrb_chrom.py +1 -1
  8. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/CpG_distrb_gene_centered.py +1 -1
  9. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/CpG_distrb_region.py +1 -3
  10. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/CpG_logo.py +1 -1
  11. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/CpG_to_gene.py +1 -1
  12. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_PCA.py +31 -23
  13. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_UMAP.py +29 -22
  14. cpgtools-2.0.2.data/scripts/beta_imputation.py +604 -0
  15. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_jitter_plot.py +1 -1
  16. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_m_conversion.py +1 -1
  17. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_profile_gene_centered.py +1 -1
  18. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_profile_region.py +1 -1
  19. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_selectNBest.py +9 -6
  20. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_stacked_barplot.py +1 -1
  21. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_stats.py +1 -1
  22. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_tSNE.py +31 -24
  23. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_topN.py +1 -1
  24. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/beta_trichotmize.py +1 -1
  25. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/dmc_Bayes.py +1 -1
  26. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/dmc_bb.py +1 -1
  27. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/dmc_fisher.py +1 -1
  28. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/dmc_glm.py +1 -1
  29. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/dmc_logit.py +1 -1
  30. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/dmc_nonparametric.py +1 -1
  31. {cpgtools-2.0.0.data → cpgtools-2.0.2.data}/scripts/dmc_ttest.py +1 -1
  32. cpgtools-2.0.2.data/scripts/predict_sex.py +126 -0
  33. cpgtools-2.0.2.dist-info/LICENSE +19 -0
  34. cpgtools-2.0.2.dist-info/METADATA +76 -0
  35. cpgtools-2.0.2.dist-info/RECORD +82 -0
  36. {cpgtools-2.0.0.dist-info → cpgtools-2.0.2.dist-info}/WHEEL +1 -1
  37. cpgtools-2.0.2.dist-info/top_level.txt +3 -0
  38. impyute/__init__.py +3 -0
  39. impyute/contrib/__init__.py +7 -0
  40. impyute/contrib/compare.py +69 -0
  41. impyute/contrib/count_missing.py +30 -0
  42. impyute/contrib/describe.py +63 -0
  43. impyute/cs/__init__.py +11 -0
  44. impyute/cs/buck_iterative.py +82 -0
  45. impyute/cs/central_tendency.py +84 -0
  46. impyute/cs/em.py +52 -0
  47. impyute/cs/fast_knn.py +130 -0
  48. impyute/cs/random.py +27 -0
  49. impyute/dataset/__init__.py +6 -0
  50. impyute/dataset/base.py +137 -0
  51. impyute/dataset/corrupt.py +55 -0
  52. impyute/deletion/__init__.py +5 -0
  53. impyute/deletion/complete_case.py +21 -0
  54. impyute/ops/__init__.py +12 -0
  55. impyute/ops/error.py +9 -0
  56. impyute/ops/inverse_distance_weighting.py +31 -0
  57. impyute/ops/matrix.py +47 -0
  58. impyute/ops/testing.py +20 -0
  59. impyute/ops/util.py +76 -0
  60. impyute/ops/wrapper.py +179 -0
  61. impyute/ts/__init__.py +6 -0
  62. impyute/ts/locf.py +57 -0
  63. impyute/ts/moving_window.py +128 -0
  64. missingpy/__init__.py +4 -0
  65. missingpy/knnimpute.py +328 -0
  66. missingpy/missforest.py +556 -0
  67. missingpy/pairwise_external.py +315 -0
  68. missingpy/tests/__init__.py +0 -0
  69. missingpy/tests/test_knnimpute.py +605 -0
  70. missingpy/tests/test_missforest.py +409 -0
  71. missingpy/utils.py +124 -0
  72. cpgmodule/data/AltumAge_cpg.pkl +0 -0
  73. cpgmodule/data/AltumAge_multi_platform_cpgs.pkl +0 -0
  74. cpgmodule/data/AltumAge_scaler.pkl +0 -0
  75. cpgmodule/data/GA_Bohlin.pkl +0 -0
  76. cpgmodule/data/GA_Haftorn.pkl +0 -0
  77. cpgmodule/data/GA_Knight.pkl +0 -0
  78. cpgmodule/data/GA_Lee_CPC.pkl +0 -0
  79. cpgmodule/data/GA_Lee_RPC.pkl +0 -0
  80. cpgmodule/data/GA_Lee_refined_RPC.pkl +0 -0
  81. cpgmodule/data/GA_Mayne.pkl +0 -0
  82. cpgmodule/data/Hannum.pkl +0 -0
  83. cpgmodule/data/Horvath_2013.pkl +0 -0
  84. cpgmodule/data/Horvath_2018.pkl +0 -0
  85. cpgmodule/data/Levine.pkl +0 -0
  86. cpgmodule/data/Lu_DNAmTL.pkl +0 -0
  87. cpgmodule/data/Ped_McEwen.pkl +0 -0
  88. cpgmodule/data/Ped_Wu.pkl +0 -0
  89. cpgmodule/data/Zhang_BLUP.pkl +0 -0
  90. cpgmodule/data/Zhang_EN.pkl +0 -0
  91. cpgtools-2.0.0.dist-info/LICENSE.txt +0 -674
  92. cpgtools-2.0.0.dist-info/METADATA +0 -28
  93. cpgtools-2.0.0.dist-info/RECORD +0 -64
  94. cpgtools-2.0.0.dist-info/top_level.txt +0 -2
cpgtools-2.0.0.dist-info/METADATA DELETED
@@ -1,28 +0,0 @@
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- Metadata-Version: 2.1
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- Name: cpgtools
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- Version: 2.0.0
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- Summary: Tools to analyze and visualize DNA methylation data
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- Home-page: https://cpgtools.readthedocs.io/en/latest/index.html
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- Author: Liguo Wang
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- Author-email: wangliguo78@gmail.com
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- Keywords: DNA methylation,CpG,bisulfite sequencing,RRBS,850K,450K
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- Platform: Linux
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- Platform: MacOS
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- Classifier: Development Status :: 5 - Production/Stable
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- Classifier: Environment :: Console
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- Classifier: Intended Audience :: Science/Research
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- Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
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- Classifier: Operating System :: MacOS :: MacOS X
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- Classifier: Operating System :: POSIX
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- Classifier: Programming Language :: Python
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- Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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- Requires-Python: >=3.5
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- License-File: LICENSE.txt
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- Requires-Dist: numpy
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- Requires-Dist: scipy
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- Requires-Dist: scikit-learn
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- Requires-Dist: weblogo
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- Requires-Dist: bx-python
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- Requires-Dist: pandas
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- Requires-Dist: umap-learn
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-
cpgtools-2.0.0.dist-info/RECORD DELETED
@@ -1,64 +0,0 @@
1
- cpgmodule/BED.py,sha256=ZNAhGZPFMFD4UpVwGTDOM0hMLnfXF52zerdMb21sH6s,12675
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- cpgmodule/MI.py,sha256=pkUWzKXYeyRuGsGKZdFVxHzFWikkuJavdQ_4fsnN3U4,8649
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- cpgmodule/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
4
- cpgmodule/cgID.py,sha256=DLG5Djm6JP0d6MiFvP_keUXv_rYxESWrISuVClTs8kw,16017914
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- cpgmodule/extend_bed.py,sha256=sjRxbRJFRumjYHwd6_AMTAYBG29yXQPYp1lDjTv2Q_Q,4648
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- cpgmodule/imotif.py,sha256=j7_MQFnowGsVTGCRQHHLUnEzSD0HehZPEHKKZ68Jv24,9227
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- cpgmodule/ireader.py,sha256=NRTdFnQvd1AEkYchfgvTVTixBVwUjn8xNyswc0OWU1Q,720
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- cpgmodule/methylClock.py,sha256=HyMk3vpVwR3yrkLCPv9fVJs6JCeSchbJEBe7i69jdSs,1202
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- cpgmodule/padjust.py,sha256=mvbQ9_crn_S39yvWrv_JPoU5OxZGHaw7cV3deBxTPdk,2389
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- cpgmodule/region2gene.py,sha256=iuSYa2-ki-qbL1TqqAlTXGT7g-j1uNIA1y7hzMwVM2U,5347
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- cpgmodule/utils.py,sha256=sPqkWK5yOWs0gN7X8Ij6AVg-2yl1CaoV98Zj_2WBryM,15031
12
- cpgmodule/data/AltumAge_cpg.pkl,sha256=T0pfBWrzQO00-z85QNE2CP0ntU0mtF2WkZeEPiArqTw,264691
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- cpgmodule/data/AltumAge_multi_platform_cpgs.pkl,sha256=Bo7ZG6AuxXUmLH6dCFfrlYkiTkeLjyqRgcD7yw4mNZ0,264816
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- cpgmodule/data/AltumAge_scaler.pkl,sha256=aDMcC4l0wZJGDi6_MeSpdNoykndfgsUtVKEd6mKf9T0,325509
15
- cpgmodule/data/GA_Bohlin.pkl,sha256=W72ra6APUZDNPmVJ-kRuaVzpiKGgI_K7nDqSFx3nf3w,2667
16
- cpgmodule/data/GA_Haftorn.pkl,sha256=ZFCJ2h0DWEaa-pHKdsSuWbQGL1JMwDXBtDyhx9DlZLc,4622
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- cpgmodule/data/GA_Knight.pkl,sha256=dsKeIt7PxCcw_tcVObtVKB3KqtF7bPH-vQqbClWI5Tc,25322
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- cpgmodule/data/GA_Lee_CPC.pkl,sha256=WfeI1bGnIS5_AIX7qnspyGYUgzGOAJ9JJ9CGQjLgkFo,25373
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- cpgmodule/data/GA_Lee_RPC.pkl,sha256=rLhr-sboWqIZ6Y08zODh7bgwXBa4SNkE4ZZaIyQTaYc,25382
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- cpgmodule/data/GA_Lee_refined_RPC.pkl,sha256=bXiZIgFSoX7Sr0ai1zHzGXv-EMGBglvx8z5vr3IpccA,25348
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- cpgmodule/data/GA_Mayne.pkl,sha256=CUfwiVIywJZwTb0PhRuW-6TQ5H1kO7tR6KHepyzBULg,1899
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- cpgmodule/data/Hannum.pkl,sha256=gXJxy6S8lBCUdr_T7ZM3R6hqKI22yev5-2giCPCCdLc,2049
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- cpgmodule/data/Horvath_2013.pkl,sha256=qwP614VYmmaESKanQ680sYgaHSWJrP73im_f5duzKgU,8313
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- cpgmodule/data/Horvath_2018.pkl,sha256=IQcFNIg-z-Mrq8vEoHI509c64Dt1wtyHInU9YwsYP-w,9225
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- cpgmodule/data/Levine.pkl,sha256=OhasOuEAvbDblZfGGFmu82kDqdo5CQ2DjZ8hfCofhvI,11751
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- cpgmodule/data/Lu_DNAmTL.pkl,sha256=SdjT9x8A0GbnKoMlDhgslmmINJ8e5Asyk9KQlw_EtJo,3548
27
- cpgmodule/data/Ped_McEwen.pkl,sha256=-hxOAqFUxORmPLV_FKYZxjOFtabxPzbbzfY6JTitq8k,2654
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- cpgmodule/data/Ped_Wu.pkl,sha256=gjXtpdpQ8QVJs1I6UM-VPAvQjNd-JDoy5DzDL-gP-Cg,2924
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- cpgmodule/data/Zhang_BLUP.pkl,sha256=dpH0L3qTxMAJ50XtTeNMmqx1khZkZyrH204E37fE37E,7038226
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- cpgmodule/data/Zhang_EN.pkl,sha256=RFEOmBQGXZvIwQ7tOYT8itOPU87V2Y02vJA2PfY6TnI,11844
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- cpgmodule/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
32
- cpgtools-2.0.0.data/scripts/CpG_aggregation.py,sha256=1n1wiXaSrbTKmqkpB_y5kxn12OCnK5WQg8Y2bLju9xg,7255
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- cpgtools-2.0.0.data/scripts/CpG_anno_position.py,sha256=bbnYshfoySpQxJZZEDtEx1-a1u1vNeJgGemchotwk8o,4620
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- cpgtools-2.0.0.data/scripts/CpG_anno_probe.py,sha256=9BY6C7GXbEnlswSgWf0MUm9y0rFDuwf9KbfTTzJ-hYM,3149
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- cpgtools-2.0.0.data/scripts/CpG_density_gene_centered.py,sha256=bFa-IpqERbBySZZZwNDhitwGz_BhfXClmxJKxQvJZ2Y,5243
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- cpgtools-2.0.0.data/scripts/CpG_distrb_chrom.py,sha256=ejeZssEC9-Sgy0vaVOVnasqCP0DdWk2AaDzqFvpLD3U,6184
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- cpgtools-2.0.0.data/scripts/CpG_distrb_gene_centered.py,sha256=K5huzI0kTD2CUsxKZwf4rG14N_uTbUMtrrZe984-Uj4,7713
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- cpgtools-2.0.0.data/scripts/CpG_distrb_region.py,sha256=GuGjtQH84_kCkW-Np-eS0xT2_6j8IXNTODaSXt0BLaA,5380
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- cpgtools-2.0.0.data/scripts/CpG_logo.py,sha256=J8DxrNToydniFh_H0AfdZYynR9nTjdfZD_NOllIuJZo,4574
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- cpgtools-2.0.0.data/scripts/CpG_to_gene.py,sha256=TQ3Cp-FFtBxY_17B1p7vKDgaF6tyD46JnDlkopEktFE,6091
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- cpgtools-2.0.0.data/scripts/beta_PCA.py,sha256=JhfXJYEp52on-lqcgRlM5mhKAGityMiYFhQO3UwNN2s,6473
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- cpgtools-2.0.0.data/scripts/beta_UMAP.py,sha256=MGDwmzE6Xj-51N55zlbWAVTB2O3tt-cu6MATZgjLU1c,7649
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- cpgtools-2.0.0.data/scripts/beta_jitter_plot.py,sha256=Ei9aBA3Hgi1ose6UtxwBIj7TsnjfNMzMgtQKHf-lRsQ,4366
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- cpgtools-2.0.0.data/scripts/beta_m_conversion.py,sha256=vfo_ME1fMZmwvX4IrIorE6PVs-Ma6mWznBUCh_AvMNo,2825
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- cpgtools-2.0.0.data/scripts/beta_profile_gene_centered.py,sha256=gp8i7z49sgBDyKGu_VE0DiGuz-_ItpY6fNHdXRw-SNk,7289
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- cpgtools-2.0.0.data/scripts/beta_profile_region.py,sha256=9h-igxQetqFXXxCLGbRC7_9IiFUUx0R3WbTjDpweW9U,5948
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- cpgtools-2.0.0.data/scripts/beta_selectNBest.py,sha256=e16UJp2odbdrpzkPcs8ul6odtV54U0SJIsCa46i2GU8,4503
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- cpgtools-2.0.0.data/scripts/beta_stacked_barplot.py,sha256=rIcSqfyWCBfFIgNIjzGdJcWn8xEObRDTxdLrvPQkVDI,3392
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- cpgtools-2.0.0.data/scripts/beta_stats.py,sha256=MlwuBMJeH1Bb5OvCTxxiMQ3cjgwTITpKgvCmotf9Zr4,2998
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- cpgtools-2.0.0.data/scripts/beta_tSNE.py,sha256=evWDAHPwzqQ4OkcBvJmRsiSut2-ypK2ABRovOOafbMI,8075
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- cpgtools-2.0.0.data/scripts/beta_topN.py,sha256=q04m9YbetU5QW_NQE28a48u-eeyl66yMi0jE31M6Lls,3891
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- cpgtools-2.0.0.data/scripts/beta_trichotmize.py,sha256=sqjFWhau89BhHeZjREnn-H_INHjiDVKqJ4UsVH6exqE,7120
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- cpgtools-2.0.0.data/scripts/dmc_Bayes.py,sha256=gO_BwLKVBBqiobrs8qZK--Yy2Mq0BA7uaG6PPXnDMFM,13712
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- cpgtools-2.0.0.data/scripts/dmc_bb.py,sha256=S1VR7YGf6f7jxrIj0xnWcHBaI6mL3ZtV1XO2GBhmdqQ,8384
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- cpgtools-2.0.0.data/scripts/dmc_fisher.py,sha256=J23sfHaFcGvItMbZSckKY4mvzaNfKyP3Tj8foJk0CmM,5140
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- cpgtools-2.0.0.data/scripts/dmc_glm.py,sha256=3dRTijWw3p2YDuMRGTvbxymsUT06Ct_JOBoLkV2Us_k,6493
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- cpgtools-2.0.0.data/scripts/dmc_logit.py,sha256=3Y5bI5yC_Binhfi7GYrqGa8NR8BJMEeVYcBajFABuKk,8465
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- cpgtools-2.0.0.data/scripts/dmc_nonparametric.py,sha256=79xeEe2SQbZ64qJ5x5NFeFoNt3wT1xwHIvVIxPaSObY,4922
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- cpgtools-2.0.0.data/scripts/dmc_ttest.py,sha256=gTiJui0u5zsaBzOIGdKIT9jXXQoG1gV3jPpZxzwSJpQ,6681
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- cpgtools-2.0.0.dist-info/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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- cpgtools-2.0.0.dist-info/METADATA,sha256=H_vHXNwUpAv4S_3hC5TclrARNBakJWXUOYQ5ZM_ABPE,957
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- cpgtools-2.0.0.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
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- cpgtools-2.0.0.dist-info/top_level.txt,sha256=NDT15C-BycDWPpPk5-3iaQdZ9JJeiOYTN7un2G3v0V8,21
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- cpgtools-2.0.0.dist-info/RECORD,,
cpgtools-2.0.0.dist-info/top_level.txt DELETED
@@ -1,2 +0,0 @@
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- cpgmodule
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- psyco_full