cpgtools 1.12.0__py3-none-any.whl → 2.0.2__py3-none-any.whl

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Files changed (77) hide show
  1. cpgmodule/_version.py +1 -0
  2. cpgmodule/data/__init__.py +0 -0
  3. cpgmodule/methylClock.py +53 -0
  4. cpgmodule/utils.py +38 -1
  5. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/CpG_aggregation.py +1 -1
  6. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/CpG_anno_position.py +1 -1
  7. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/CpG_anno_probe.py +6 -4
  8. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/CpG_density_gene_centered.py +1 -1
  9. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/CpG_distrb_chrom.py +1 -1
  10. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/CpG_distrb_gene_centered.py +1 -1
  11. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/CpG_distrb_region.py +1 -3
  12. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/CpG_logo.py +1 -1
  13. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/CpG_to_gene.py +1 -1
  14. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_PCA.py +31 -23
  15. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_UMAP.py +29 -22
  16. cpgtools-2.0.2.data/scripts/beta_imputation.py +604 -0
  17. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_jitter_plot.py +1 -1
  18. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_m_conversion.py +1 -1
  19. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_profile_gene_centered.py +1 -1
  20. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_profile_region.py +1 -1
  21. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_selectNBest.py +9 -6
  22. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_stacked_barplot.py +1 -1
  23. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_stats.py +1 -1
  24. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_tSNE.py +31 -24
  25. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_topN.py +1 -1
  26. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/beta_trichotmize.py +1 -1
  27. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/dmc_Bayes.py +1 -1
  28. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/dmc_bb.py +1 -1
  29. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/dmc_fisher.py +1 -1
  30. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/dmc_glm.py +1 -1
  31. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/dmc_logit.py +1 -1
  32. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/dmc_nonparametric.py +1 -1
  33. {cpgtools-1.12.0.data → cpgtools-2.0.2.data}/scripts/dmc_ttest.py +3 -3
  34. cpgtools-2.0.2.data/scripts/predict_sex.py +126 -0
  35. cpgtools-2.0.2.dist-info/LICENSE +19 -0
  36. cpgtools-2.0.2.dist-info/METADATA +76 -0
  37. cpgtools-2.0.2.dist-info/RECORD +82 -0
  38. {cpgtools-1.12.0.dist-info → cpgtools-2.0.2.dist-info}/WHEEL +1 -1
  39. cpgtools-2.0.2.dist-info/top_level.txt +3 -0
  40. impyute/__init__.py +3 -0
  41. impyute/contrib/__init__.py +7 -0
  42. impyute/contrib/compare.py +69 -0
  43. impyute/contrib/count_missing.py +30 -0
  44. impyute/contrib/describe.py +63 -0
  45. impyute/cs/__init__.py +11 -0
  46. impyute/cs/buck_iterative.py +82 -0
  47. impyute/cs/central_tendency.py +84 -0
  48. impyute/cs/em.py +52 -0
  49. impyute/cs/fast_knn.py +130 -0
  50. impyute/cs/random.py +27 -0
  51. impyute/dataset/__init__.py +6 -0
  52. impyute/dataset/base.py +137 -0
  53. impyute/dataset/corrupt.py +55 -0
  54. impyute/deletion/__init__.py +5 -0
  55. impyute/deletion/complete_case.py +21 -0
  56. impyute/ops/__init__.py +12 -0
  57. impyute/ops/error.py +9 -0
  58. impyute/ops/inverse_distance_weighting.py +31 -0
  59. impyute/ops/matrix.py +47 -0
  60. impyute/ops/testing.py +20 -0
  61. impyute/ops/util.py +76 -0
  62. impyute/ops/wrapper.py +179 -0
  63. impyute/ts/__init__.py +6 -0
  64. impyute/ts/locf.py +57 -0
  65. impyute/ts/moving_window.py +128 -0
  66. missingpy/__init__.py +4 -0
  67. missingpy/knnimpute.py +328 -0
  68. missingpy/missforest.py +556 -0
  69. missingpy/pairwise_external.py +315 -0
  70. missingpy/tests/__init__.py +0 -0
  71. missingpy/tests/test_knnimpute.py +605 -0
  72. missingpy/tests/test_missforest.py +409 -0
  73. missingpy/utils.py +124 -0
  74. cpgtools-1.12.0.dist-info/LICENSE.txt +0 -674
  75. cpgtools-1.12.0.dist-info/METADATA +0 -30
  76. cpgtools-1.12.0.dist-info/RECORD +0 -43
  77. cpgtools-1.12.0.dist-info/top_level.txt +0 -2
cpgtools-1.12.0.dist-info/METADATA DELETED
@@ -1,30 +0,0 @@
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- Metadata-Version: 2.1
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- Name: cpgtools
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- Version: 1.12.0
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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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- License: UNKNOWN
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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: sklearn
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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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-
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- UNKNOWN
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-
cpgtools-1.12.0.dist-info/RECORD DELETED
@@ -1,43 +0,0 @@
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- 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
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- 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/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=cNvfNCKg1PWBOb9kpMOsfYHI9Y-0q1di8znx4kr3Vhs,14986
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- cpgtools-1.12.0.data/scripts/CpG_aggregation.py,sha256=Y1FTmgBy_l4_6zvZUgXrvO_s9tTVyx_q8kM9hP7KF20,7256
12
- cpgtools-1.12.0.data/scripts/CpG_anno_position.py,sha256=bbnYshfoySpQxJZZEDtEx1-a1u1vNeJgGemchotwk8o,4620
13
- cpgtools-1.12.0.data/scripts/CpG_anno_probe.py,sha256=xrAybzTPIRhZ8HrA3V3T-fzUz6heOzffz_Wqa0XCd_8,3064
14
- cpgtools-1.12.0.data/scripts/CpG_density_gene_centered.py,sha256=nmByBbMbpQslm-NhQnCL8G8avCOGbBek8scaP2MWqZA,5244
15
- cpgtools-1.12.0.data/scripts/CpG_distrb_chrom.py,sha256=5yk03G6hC8pd_CSQPCfVQZEh6sJ6yWJ798Rp45uVVmE,6185
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- cpgtools-1.12.0.data/scripts/CpG_distrb_gene_centered.py,sha256=auho1AykMw8oUqsuCC_B7-OuEGd_TgUV22V4_YR6Ai0,7714
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- cpgtools-1.12.0.data/scripts/CpG_distrb_region.py,sha256=MgeHTMaEfulnx-5w3mCo1zjaaPeclvx3SvCHZugsZ_Q,5381
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- cpgtools-1.12.0.data/scripts/CpG_logo.py,sha256=uyydTbK3cbKqxDkDkHk8sxRrQr9EZCs4mKPZ5nOHW20,4575
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- cpgtools-1.12.0.data/scripts/CpG_to_gene.py,sha256=scT5mkVt4ydvKntpx8ChWOmf8dE2rmJ-w-9Xziw2SMo,6092
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- cpgtools-1.12.0.data/scripts/beta_PCA.py,sha256=HAGrXjTZbM8t2cea5cq8KmX87UQDggrFFeirjM8h71w,6474
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- cpgtools-1.12.0.data/scripts/beta_UMAP.py,sha256=nSIM8DU-bbubNKh-qLtDPzcgswP-E1T_1YbHQGPE2EQ,7650
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- cpgtools-1.12.0.data/scripts/beta_jitter_plot.py,sha256=7pT0AQrw_Hj1B_bEKdkxoSVsS6Ev9-jOlAczCMgwllo,4367
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- cpgtools-1.12.0.data/scripts/beta_m_conversion.py,sha256=nUI9VC4HeT84rXCCN7SddM-ekdZ5yJShcvrhgIZ0C1c,2826
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- cpgtools-1.12.0.data/scripts/beta_profile_gene_centered.py,sha256=M_1vndWlpoh68qdcxYY3est5BduKQY7dfcrAhMhoA8o,7290
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- cpgtools-1.12.0.data/scripts/beta_profile_region.py,sha256=Iil1fUq8c_mESLJtiFFUS3McQAgRPA3AitLek_Aa-jE,5949
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- cpgtools-1.12.0.data/scripts/beta_selectNBest.py,sha256=R70Qe9TW0cImBqnApRzb906_mMNvS8Opw6p7MWraRvs,4504
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- cpgtools-1.12.0.data/scripts/beta_stacked_barplot.py,sha256=-QOnvBbjHsyaCOwf5uo8C5p_tgo_hCYOAdI0Ml9WGsA,3393
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- cpgtools-1.12.0.data/scripts/beta_stats.py,sha256=T3-Fp-djNx96XDVJSkYnjjXhoqPSx9HhuqqbuZlLU3s,2999
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- cpgtools-1.12.0.data/scripts/beta_tSNE.py,sha256=2RUyKuMDL3-yejbjTSULBKVAIzk-0n1edhp4RhK_3ps,8076
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- cpgtools-1.12.0.data/scripts/beta_topN.py,sha256=0Yq4Z_oACfaUBYRjMghBCzXg4hC6l7l9Pxk0_oNKo9g,3892
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- cpgtools-1.12.0.data/scripts/beta_trichotmize.py,sha256=p9DLb4VQyIbuzJuNud0PJKKfTN_inr-eRhE5bbEim8c,7121
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- cpgtools-1.12.0.data/scripts/dmc_Bayes.py,sha256=9y23nbzdzmnfq-gmoD0EBnWR2ilzqWC5b6QIuTX7c9I,13713
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- cpgtools-1.12.0.data/scripts/dmc_bb.py,sha256=WkGpUBPDt8PWEXwzbpRAp1YV9Sf8o5RXjkb2m6ZJ8eI,8385
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- cpgtools-1.12.0.data/scripts/dmc_fisher.py,sha256=cjypMyg7qF57AdEbZ3CGgYsjQ9llKzKG_D77rP1tSCI,5141
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- cpgtools-1.12.0.data/scripts/dmc_glm.py,sha256=PoTQGAi27wTmlzD8v9Mwf3sy1p559EXqwQY1frE2rPM,6494
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- cpgtools-1.12.0.data/scripts/dmc_logit.py,sha256=_SLVYbVZfs9uHqnsLpp5Ttix66t2nwADszulJ4GL8uY,8466
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- cpgtools-1.12.0.data/scripts/dmc_nonparametric.py,sha256=eOL0yUGBS4DhesH5xGL0JLBXVSDzhU9-kOhwDLv0RWg,4923
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- cpgtools-1.12.0.data/scripts/dmc_ttest.py,sha256=7Kn7d85HBKXKror2ms2Ds7CsBEnwSMn8IsIIZ2M1PMA,6632
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- cpgtools-1.12.0.dist-info/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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- cpgtools-1.12.0.dist-info/METADATA,sha256=MtpoP_KMFs85FziKXsmuArtItTvETFYKudWC7jeAiWA,953
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- cpgtools-1.12.0.dist-info/WHEEL,sha256=g4nMs7d-Xl9-xC9XovUrsDHGXt-FT0E17Yqo92DEfvY,92
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- cpgtools-1.12.0.dist-info/top_level.txt,sha256=NDT15C-BycDWPpPk5-3iaQdZ9JJeiOYTN7un2G3v0V8,21
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- cpgtools-1.12.0.dist-info/RECORD,,
cpgtools-1.12.0.dist-info/top_level.txt DELETED
@@ -1,2 +0,0 @@
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- cpgmodule
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- psyco_full