biopipen 0.21.2__py3-none-any.whl → 0.22.1__py3-none-any.whl

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Files changed (62) hide show
  1. biopipen/__init__.py +1 -1
  2. biopipen/core/filters.py +142 -0
  3. biopipen/ns/scrna.py +19 -1
  4. biopipen/ns/tcr.py +30 -10
  5. biopipen/reports/delim/SampleInfo.svelte +2 -22
  6. biopipen/reports/scrna/CellsDistribution.svelte +4 -39
  7. biopipen/reports/scrna/MarkersFinder.svelte +6 -126
  8. biopipen/reports/scrna/MetaMarkers.svelte +3 -75
  9. biopipen/reports/scrna/RadarPlots.svelte +4 -20
  10. biopipen/reports/scrna/ScFGSEA.svelte +4 -23
  11. biopipen/reports/scrna/SeuratClusterStats.svelte +3 -69
  12. biopipen/reports/scrna/SeuratPreparing.svelte +3 -26
  13. biopipen/reports/scrna/TopExpressingGenes.svelte +3 -41
  14. biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte +17 -16
  15. biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.svelte +13 -16
  16. biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte +44 -52
  17. biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte +2 -8
  18. biopipen/reports/tcr/CDR3AAPhyschem.svelte +18 -65
  19. biopipen/reports/tcr/CloneResidency.svelte +3 -93
  20. biopipen/reports/tcr/Immunarch.svelte +4 -168
  21. biopipen/reports/tcr/TCRClusterStats.svelte +3 -45
  22. biopipen/reports/tcr/TESSA.svelte +11 -28
  23. biopipen/scripts/delim/SampleInfo.R +41 -7
  24. biopipen/scripts/scrna/CellsDistribution.R +127 -16
  25. biopipen/scripts/scrna/MarkersFinder.R +245 -100
  26. biopipen/scripts/scrna/MetaMarkers.R +163 -82
  27. biopipen/scripts/scrna/RadarPlots.R +163 -110
  28. biopipen/scripts/scrna/ScFGSEA.R +51 -11
  29. biopipen/scripts/scrna/SeuratClusterStats-dimplots.R +26 -13
  30. biopipen/scripts/scrna/SeuratClusterStats-features.R +58 -53
  31. biopipen/scripts/scrna/SeuratClusterStats-stats.R +39 -21
  32. biopipen/scripts/scrna/SeuratClusterStats.R +4 -2
  33. biopipen/scripts/scrna/SeuratClustering.R +73 -26
  34. biopipen/scripts/scrna/SeuratMetadataMutater.R +13 -1
  35. biopipen/scripts/scrna/SeuratPreparing.R +93 -19
  36. biopipen/scripts/scrna/TopExpressingGenes.R +100 -18
  37. biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R +21 -8
  38. biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R +25 -3
  39. biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R +1 -0
  40. biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R +14 -3
  41. biopipen/scripts/tcr/Attach2Seurat.R +2 -1
  42. biopipen/scripts/tcr/CDR3AAPhyschem.R +123 -10
  43. biopipen/scripts/tcr/CloneResidency.R +114 -34
  44. biopipen/scripts/tcr/Immunarch-basic.R +18 -4
  45. biopipen/scripts/tcr/Immunarch-clonality.R +14 -0
  46. biopipen/scripts/tcr/Immunarch-diversity.R +123 -18
  47. biopipen/scripts/tcr/Immunarch-geneusage.R +23 -1
  48. biopipen/scripts/tcr/Immunarch-kmer.R +45 -3
  49. biopipen/scripts/tcr/Immunarch-overlap.R +62 -0
  50. biopipen/scripts/tcr/Immunarch-spectratyping.R +18 -2
  51. biopipen/scripts/tcr/Immunarch-tracking.R +24 -1
  52. biopipen/scripts/tcr/Immunarch-vjjunc.R +17 -2
  53. biopipen/scripts/tcr/Immunarch.R +7 -0
  54. biopipen/scripts/tcr/ImmunarchLoading.R +22 -23
  55. biopipen/scripts/tcr/TCRClusterStats.R +124 -11
  56. biopipen/scripts/tcr/TCRClustering.R +8 -9
  57. biopipen/scripts/tcr/TESSA.R +66 -41
  58. biopipen/utils/misc.R +96 -1
  59. {biopipen-0.21.2.dist-info → biopipen-0.22.1.dist-info}/METADATA +1 -1
  60. {biopipen-0.21.2.dist-info → biopipen-0.22.1.dist-info}/RECORD +62 -62
  61. {biopipen-0.21.2.dist-info → biopipen-0.22.1.dist-info}/WHEEL +0 -0
  62. {biopipen-0.21.2.dist-info → biopipen-0.22.1.dist-info}/entry_points.txt +0 -0
@@ -1,9 +1,9 @@
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- biopipen/__init__.py,sha256=Br99nmRrjyPtE6zPC2M_-gnaJCaBkqZI2lE8zWDjxpQ,23
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+ biopipen/__init__.py,sha256=mjWPUw5WSKjOdLE532eMicR6Gvc0AStLxFjzYGRWcns,23
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  biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
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  biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
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- biopipen/core/filters.py,sha256=NSeEElvRujLZQTV1e4zmQXZb2RjaAvGt1AaRH_xUOTA,7061
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+ biopipen/core/filters.py,sha256=5Qi7do0JT8_mwd80ddf4TgsX7yZh__ZpOex270Jjrbc,11037
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  biopipen/core/proc.py,sha256=7TsjBM7EEtMMB-w4jbxV_CSRY8J970gM8320Ga1YeHU,717
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  biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -19,11 +19,11 @@ biopipen/ns/gsea.py,sha256=EsNRAPYsagaV2KYgr4Jv0KCnZGqayM209v4yOGGTIOI,7423
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- biopipen/ns/scrna.py,sha256=-ZtoSfnbKnlulgyr3I2_b0hRkUEoOH8V_1ZkEpdSlGY,81407
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+ biopipen/ns/scrna.py,sha256=F5j1TmjsS2swwm-uDyT6sTys5pldIJ_M2hNITAQdflc,82728
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  biopipen/ns/scrna_basic.py,sha256=Py90IveDI5Alm6FUeC89xp3W79VPRvAQctQpc5JtO2M,8639
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  biopipen/ns/scrna_metabolic_landscape.py,sha256=dSL-y1Gx1fcgebX7vk3wcSbm9aBALfCZKz0vjcDxQ_8,28139
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  biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
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- biopipen/ns/tcr.py,sha256=-cHx2VjfcYUIwWh1OpEfjHDe3RPH-GDlLnpS4pljUs8,82417
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+ biopipen/ns/tcr.py,sha256=ZCwL_1Of-F5xVJ0hgdVLAjHwwwfegqkW_SO66oYULqM,83738
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@@ -35,30 +35,30 @@ biopipen/reports/cnv/TMADScoreSummary.svelte,sha256=tJutaMOqeXxKroAosOIqOJVyhTTF
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- biopipen/reports/delim/SampleInfo.svelte,sha256=KJsukqPgkebUE8MlKIsl9mfj9d-Z2_JBt1wOx8RylDo,958
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+ biopipen/reports/delim/SampleInfo.svelte,sha256=Vpjrdd3AXNDNhx2pzDaFA61xPMYAFKvvIoVCqUswiyo,365
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- biopipen/reports/scrna/CellsDistribution.svelte,sha256=Lam6Vqn-C3QcKy1wKgxnnFzwKOodSm041tFfZ5A8agQ,2015
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+ biopipen/reports/scrna/CellsDistribution.svelte,sha256=Mg6P0tazpzOxsOAtc-0LGEim5KprPt5KIgoW3TzrxxA,413
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  biopipen/reports/scrna/DimPlots.svelte,sha256=ZLbtN0ioevRyEky4jb_DkDGAcpy_jAhaHfFym5ELEPM,479
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- biopipen/reports/scrna/MarkersFinder.svelte,sha256=0xyOA6eCrtgfCxJ_Tkhc5ZlKK10MyzRsuW21VRPyks4,5858
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- biopipen/reports/scrna/MetaMarkers.svelte,sha256=mPdwV9sTXn6fLTZWqTvFNSn7fdIs-7w4HSerV69o6C0,3709
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- biopipen/reports/scrna/RadarPlots.svelte,sha256=QnqQ5J-27KR5apcKmP10fDkoAyO9n3Q2LPEWqDuRxdw,1075
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- biopipen/reports/scrna/ScFGSEA.svelte,sha256=uLOlfillgvLbDCO7CzIKZ3HzwO4fZcCcJOpzJRnKwm4,1268
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- biopipen/reports/scrna/SeuratClusterStats.svelte,sha256=_vRaffYxpPh_Zdw1O-U7zKkZTUHtrugyhuT7REYaWEk,3433
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+ biopipen/reports/scrna/MarkersFinder.svelte,sha256=77rD1psj0VJykPDhfwS-B8mubvaasREAE6RYR2atTN4,444
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+ biopipen/reports/scrna/MetaMarkers.svelte,sha256=iIFRKjvVYrM1AtDWqq8UfeS8q23R8FKg2yepKAw2KSE,508
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+ biopipen/reports/scrna/RadarPlots.svelte,sha256=g_fp9d3vdnzk-egXPhkhhfWXOeG569Rj8rYLRIKmlLc,396
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+ biopipen/reports/scrna/ScFGSEA.svelte,sha256=ggG0Yq16MWt1dj6-r1wRvt7rWYiUUgUOWP_8TAXAbhA,471
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+ biopipen/reports/scrna/SeuratClusterStats.svelte,sha256=rTsoOCiVm7lEyBYgu2ZVcKNGi4g6PynYoOSx0DHdTHo,429
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- biopipen/reports/scrna/SeuratPreparing.svelte,sha256=30luUmsqBQcuh2xl6k57j70k6KGZ5bM3IGk_i04vmuw,1114
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- biopipen/reports/scrna/TopExpressingGenes.svelte,sha256=lVvlKwMep4woYTiTPTTvlSPOycjxUb44aiEqNzj9u18,1952
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- biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=1AHjiInGLev1_gfis5oVegYXgKLzDXA9qMwEgPqRDfI,880
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- biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.svelte,sha256=XYCaO6HTQ5H5M0yWh6Pf9xzxcfwAFt9fICXBcINAOZw,993
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- biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=0rHqUyciqPq7w-5mEoQRTPrqbqszkLV8zcZjZ6UXwI4,3167
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- biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte,sha256=Aj9m2TVmjwLleFapmIY_iB5afDuTZr3s5AIm_qbQcGw,608
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- biopipen/reports/tcr/CDR3AAPhyschem.svelte,sha256=mdpD9sJxyDulLMV1Ph6IZ_OIKsHhKQjLxC4cfBJRiA8,3212
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- biopipen/reports/tcr/CloneResidency.svelte,sha256=N62tlEubCty0F6RtCH_p5UeXPf8wl8zdMgAu-P2GrOM,4284
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- biopipen/reports/tcr/Immunarch.svelte,sha256=C5Itq9sU9z5MEP5TkQuYsL9QzOfbqblRvNmSfnU6wN8,7067
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+ biopipen/reports/scrna/SeuratPreparing.svelte,sha256=CCQ3qodjfoQeMZhSZp7irvSqBt10m7urzcWEOHsZa8M,365
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+ biopipen/reports/scrna/TopExpressingGenes.svelte,sha256=h2Or2cKCzuY2cypq1PKrqiHFVMZmFUgFOXoQumvfGSk,471
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+ biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=jffsxv6YT3JgCeKLjqWxpKUC5TKj2bUfYVW7tklozU0,958
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+ biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.svelte,sha256=p5aFKwruK9GMpOts6h5BwiM0UM5II85uu7gac7nJy8I,887
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+ biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=bbPWDEXTi-A377Vo2VaEyh_VoxGmFj-P3WX8g_y_-9k,3416
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+ biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte,sha256=TohFc1IsHFAio8WNu_1FoaJucxsW3OtmS7fIJOH5KHc,350
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+ biopipen/reports/tcr/CDR3AAPhyschem.svelte,sha256=_r1pi_yTu_KjC02aegZ52IEQY8Mq0p3nqW_o9wOFWf8,1530
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+ biopipen/reports/tcr/CloneResidency.svelte,sha256=pzjkdGAhB7STxlXkTY5wnTT3plhkAPKMdGa6jwKuwoc,470
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+ biopipen/reports/tcr/Immunarch.svelte,sha256=jHOGUCWREaDNUf1_s6h9Kx_sp-y_dDRqY1rWrx0o0LM,433
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- biopipen/reports/tcr/TESSA.svelte,sha256=UI7ZeQcLAZXHJQe6pWck9_Hw3ll3YE9L0y_b0cF347Y,2508
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+ biopipen/reports/tcr/TCRClusterStats.svelte,sha256=YGK5_Vp85QmUJZO1ZGtg1IWBsh9o-z-dSYC8kuW3ssU,415
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+ biopipen/reports/tcr/TESSA.svelte,sha256=S1tG0HIU5569ybV0shuTz1CN0JcqFrFNB7M6JCiGhm0,1948
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+ biopipen/scripts/scrna/MetaMarkers.R,sha256=3gZdMjO4sGQLq0XvlLooMrQUKEAIYUCTsxVHrkYe7HM,11119
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