cpgtools 2.0.5__py3-none-any.whl

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Files changed (104) hide show
  1. cpgmodule/BED.py +441 -0
  2. cpgmodule/MI.py +193 -0
  3. cpgmodule/__init__.py +0 -0
  4. cpgmodule/_version.py +1 -0
  5. cpgmodule/cgID.py +866897 -0
  6. cpgmodule/data/AltumAge_cpg.pkl +0 -0
  7. cpgmodule/data/AltumAge_multi_platform_cpgs.pkl +0 -0
  8. cpgmodule/data/AltumAge_scaler.pkl +0 -0
  9. cpgmodule/data/GA_Bohlin.pkl +0 -0
  10. cpgmodule/data/GA_Haftorn.pkl +0 -0
  11. cpgmodule/data/GA_Knight.pkl +0 -0
  12. cpgmodule/data/GA_Lee_CPC.pkl +0 -0
  13. cpgmodule/data/GA_Lee_RPC.pkl +0 -0
  14. cpgmodule/data/GA_Lee_refined_RPC.pkl +0 -0
  15. cpgmodule/data/GA_Mayne.pkl +0 -0
  16. cpgmodule/data/Hannum.pkl +0 -0
  17. cpgmodule/data/Horvath_2013.pkl +0 -0
  18. cpgmodule/data/Horvath_2018.pkl +0 -0
  19. cpgmodule/data/Levine.pkl +0 -0
  20. cpgmodule/data/Lu_DNAmTL.pkl +0 -0
  21. cpgmodule/data/Ped_McEwen.pkl +0 -0
  22. cpgmodule/data/Ped_Wu.pkl +0 -0
  23. cpgmodule/data/Zhang_BLUP.pkl +0 -0
  24. cpgmodule/data/Zhang_EN.pkl +0 -0
  25. cpgmodule/data/__init__.py +0 -0
  26. cpgmodule/extend_bed.py +147 -0
  27. cpgmodule/imotif.py +348 -0
  28. cpgmodule/ireader.py +28 -0
  29. cpgmodule/methylClock.py +53 -0
  30. cpgmodule/padjust.py +58 -0
  31. cpgmodule/region2gene.py +170 -0
  32. cpgmodule/utils.py +642 -0
  33. cpgtools-2.0.5.data/scripts/CpG_aggregation.py +238 -0
  34. cpgtools-2.0.5.data/scripts/CpG_anno_position.py +156 -0
  35. cpgtools-2.0.5.data/scripts/CpG_anno_probe.py +112 -0
  36. cpgtools-2.0.5.data/scripts/CpG_density_gene_centered.py +107 -0
  37. cpgtools-2.0.5.data/scripts/CpG_distrb_chrom.py +154 -0
  38. cpgtools-2.0.5.data/scripts/CpG_distrb_gene_centered.py +193 -0
  39. cpgtools-2.0.5.data/scripts/CpG_distrb_region.py +146 -0
  40. cpgtools-2.0.5.data/scripts/CpG_logo.py +134 -0
  41. cpgtools-2.0.5.data/scripts/CpG_to_gene.py +141 -0
  42. cpgtools-2.0.5.data/scripts/beta_PCA.py +188 -0
  43. cpgtools-2.0.5.data/scripts/beta_UMAP.py +181 -0
  44. cpgtools-2.0.5.data/scripts/beta_combat.py +174 -0
  45. cpgtools-2.0.5.data/scripts/beta_jitter_plot.py +107 -0
  46. cpgtools-2.0.5.data/scripts/beta_m_conversion.py +105 -0
  47. cpgtools-2.0.5.data/scripts/beta_profile_gene_centered.py +165 -0
  48. cpgtools-2.0.5.data/scripts/beta_profile_region.py +152 -0
  49. cpgtools-2.0.5.data/scripts/beta_selectNBest.py +116 -0
  50. cpgtools-2.0.5.data/scripts/beta_stacked_barplot.py +119 -0
  51. cpgtools-2.0.5.data/scripts/beta_stats.py +101 -0
  52. cpgtools-2.0.5.data/scripts/beta_tSNE.py +179 -0
  53. cpgtools-2.0.5.data/scripts/beta_topN.py +99 -0
  54. cpgtools-2.0.5.data/scripts/beta_trichotmize.py +190 -0
  55. cpgtools-2.0.5.data/scripts/dmc_Bayes.py +442 -0
  56. cpgtools-2.0.5.data/scripts/dmc_bb.py +221 -0
  57. cpgtools-2.0.5.data/scripts/dmc_fisher.py +161 -0
  58. cpgtools-2.0.5.data/scripts/dmc_glm.py +191 -0
  59. cpgtools-2.0.5.data/scripts/dmc_logit.py +226 -0
  60. cpgtools-2.0.5.data/scripts/dmc_nonparametric.py +176 -0
  61. cpgtools-2.0.5.data/scripts/dmc_ttest.py +222 -0
  62. cpgtools-2.0.5.data/scripts/predict_missing.py +673 -0
  63. cpgtools-2.0.5.data/scripts/predict_sex.py +126 -0
  64. cpgtools-2.0.5.dist-info/METADATA +59 -0
  65. cpgtools-2.0.5.dist-info/RECORD +104 -0
  66. cpgtools-2.0.5.dist-info/WHEEL +5 -0
  67. cpgtools-2.0.5.dist-info/licenses/LICENSE.txt +19 -0
  68. cpgtools-2.0.5.dist-info/top_level.txt +5 -0
  69. impyute/__init__.py +3 -0
  70. impyute/contrib/__init__.py +7 -0
  71. impyute/contrib/compare.py +69 -0
  72. impyute/contrib/count_missing.py +30 -0
  73. impyute/contrib/describe.py +63 -0
  74. impyute/cs/__init__.py +11 -0
  75. impyute/cs/buck_iterative.py +82 -0
  76. impyute/cs/central_tendency.py +84 -0
  77. impyute/cs/em.py +52 -0
  78. impyute/cs/fast_knn.py +130 -0
  79. impyute/cs/random.py +27 -0
  80. impyute/dataset/__init__.py +6 -0
  81. impyute/dataset/base.py +137 -0
  82. impyute/dataset/corrupt.py +55 -0
  83. impyute/deletion/__init__.py +5 -0
  84. impyute/deletion/complete_case.py +21 -0
  85. impyute/ops/__init__.py +12 -0
  86. impyute/ops/error.py +9 -0
  87. impyute/ops/inverse_distance_weighting.py +31 -0
  88. impyute/ops/matrix.py +47 -0
  89. impyute/ops/testing.py +20 -0
  90. impyute/ops/util.py +96 -0
  91. impyute/ops/wrapper.py +179 -0
  92. impyute/ts/__init__.py +6 -0
  93. impyute/ts/locf.py +57 -0
  94. impyute/ts/moving_window.py +128 -0
  95. impyutelib.py +890 -0
  96. missingpy/__init__.py +4 -0
  97. missingpy/knnimpute.py +328 -0
  98. missingpy/missforest.py +556 -0
  99. missingpy/pairwise_external.py +315 -0
  100. missingpy/tests/__init__.py +0 -0
  101. missingpy/tests/test_knnimpute.py +605 -0
  102. missingpy/tests/test_missforest.py +409 -0
  103. missingpy/utils.py +124 -0
  104. misspylib.py +565 -0

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