biopipen 0.32.1__py3-none-any.whl → 0.33.0__py3-none-any.whl

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Files changed (134) hide show
  1. biopipen/__init__.py +1 -1
  2. biopipen/core/config.toml +6 -0
  3. biopipen/core/filters.py +77 -26
  4. biopipen/core/testing.py +6 -1
  5. biopipen/ns/bam.py +39 -0
  6. biopipen/ns/cellranger.py +5 -0
  7. biopipen/ns/cellranger_pipeline.py +2 -2
  8. biopipen/ns/cnvkit_pipeline.py +4 -1
  9. biopipen/ns/delim.py +33 -27
  10. biopipen/ns/protein.py +99 -0
  11. biopipen/ns/scrna.py +411 -250
  12. biopipen/ns/snp.py +16 -3
  13. biopipen/ns/tcr.py +125 -1
  14. biopipen/ns/vcf.py +34 -0
  15. biopipen/ns/web.py +5 -1
  16. biopipen/reports/scrna/SeuratClusterStats.svelte +1 -1
  17. biopipen/reports/scrna/SeuratMap2Ref.svelte +15 -2
  18. biopipen/reports/tcr/ClonalStats.svelte +15 -0
  19. biopipen/reports/utils/misc.liq +22 -7
  20. biopipen/scripts/bam/BamMerge.py +2 -2
  21. biopipen/scripts/bam/BamSampling.py +4 -4
  22. biopipen/scripts/bam/BamSort.py +141 -0
  23. biopipen/scripts/bam/BamSplitChroms.py +10 -10
  24. biopipen/scripts/bam/BamSubsetByBed.py +3 -3
  25. biopipen/scripts/bam/CNVpytor.py +10 -10
  26. biopipen/scripts/bam/ControlFREEC.py +11 -11
  27. biopipen/scripts/bed/Bed2Vcf.py +5 -5
  28. biopipen/scripts/bed/BedConsensus.py +5 -5
  29. biopipen/scripts/bed/BedLiftOver.sh +6 -4
  30. biopipen/scripts/bed/BedtoolsIntersect.py +4 -4
  31. biopipen/scripts/bed/BedtoolsMakeWindows.py +3 -3
  32. biopipen/scripts/bed/BedtoolsMerge.py +4 -4
  33. biopipen/scripts/cellranger/CellRangerCount.py +20 -9
  34. biopipen/scripts/cellranger/CellRangerSummary.R +20 -29
  35. biopipen/scripts/cellranger/CellRangerVdj.py +8 -8
  36. biopipen/scripts/cnvkit/CNVkitAccess.py +6 -6
  37. biopipen/scripts/cnvkit/CNVkitAutobin.py +25 -18
  38. biopipen/scripts/cnvkit/CNVkitBatch.py +5 -5
  39. biopipen/scripts/cnvkit/CNVkitCall.py +3 -3
  40. biopipen/scripts/cnvkit/CNVkitCoverage.py +2 -2
  41. biopipen/scripts/cnvkit/CNVkitDiagram.py +5 -5
  42. biopipen/scripts/cnvkit/CNVkitFix.py +3 -3
  43. biopipen/scripts/cnvkit/CNVkitGuessBaits.py +9 -5
  44. biopipen/scripts/cnvkit/CNVkitHeatmap.py +4 -4
  45. biopipen/scripts/cnvkit/CNVkitReference.py +2 -2
  46. biopipen/scripts/cnvkit/CNVkitScatter.py +5 -5
  47. biopipen/scripts/cnvkit/CNVkitSegment.py +5 -5
  48. biopipen/scripts/cnvkit/guess_baits.py +166 -93
  49. biopipen/scripts/delim/SampleInfo.R +85 -139
  50. biopipen/scripts/misc/Config2File.py +2 -2
  51. biopipen/scripts/misc/Str2File.py +2 -2
  52. biopipen/scripts/protein/MMCIF2PDB.py +33 -0
  53. biopipen/scripts/protein/PDB2Fasta.py +60 -0
  54. biopipen/scripts/protein/Prodigy.py +4 -4
  55. biopipen/scripts/protein/RMSD.py +178 -0
  56. biopipen/scripts/regulatory/MotifScan.py +8 -8
  57. biopipen/scripts/scrna/CellCellCommunication.py +59 -22
  58. biopipen/scripts/scrna/CellsDistribution.R +31 -6
  59. biopipen/scripts/scrna/MarkersFinder.R +272 -602
  60. biopipen/scripts/scrna/MetaMarkers.R +16 -7
  61. biopipen/scripts/scrna/RadarPlots.R +75 -35
  62. biopipen/scripts/scrna/SCP-plot.R +15202 -0
  63. biopipen/scripts/scrna/ScVelo.py +0 -0
  64. biopipen/scripts/scrna/SeuratClusterStats-clustree.R +23 -25
  65. biopipen/scripts/scrna/SeuratClusterStats-dimplots.R +26 -47
  66. biopipen/scripts/scrna/SeuratClusterStats-features.R +85 -385
  67. biopipen/scripts/scrna/SeuratClusterStats-ngenes.R +33 -13
  68. biopipen/scripts/scrna/SeuratClusterStats-stats.R +45 -228
  69. biopipen/scripts/scrna/SeuratClusterStats.R +13 -19
  70. biopipen/scripts/scrna/SeuratMap2Ref.R +16 -6
  71. biopipen/scripts/scrna/SeuratPreparing.R +138 -81
  72. biopipen/scripts/scrna/SlingShot.R +71 -0
  73. biopipen/scripts/scrna/TopExpressingGenes.R +9 -7
  74. biopipen/scripts/scrna/celltypist-wrapper.py +7 -6
  75. biopipen/scripts/snp/Plink2GTMat.py +26 -11
  76. biopipen/scripts/snp/PlinkFilter.py +7 -7
  77. biopipen/scripts/snp/PlinkFromVcf.py +8 -5
  78. biopipen/scripts/snp/PlinkSimulation.py +4 -4
  79. biopipen/scripts/snp/PlinkUpdateName.py +4 -4
  80. biopipen/scripts/stats/ChowTest.R +48 -22
  81. biopipen/scripts/tcgamaf/Maf2Vcf.py +2 -2
  82. biopipen/scripts/tcgamaf/MafAddChr.py +2 -2
  83. biopipen/scripts/tcr/CDR3AAPhyschem.R +12 -2
  84. biopipen/scripts/tcr/ClonalStats.R +484 -0
  85. biopipen/scripts/tcr/CloneResidency.R +23 -5
  86. biopipen/scripts/tcr/Immunarch-basic.R +8 -1
  87. biopipen/scripts/tcr/Immunarch-clonality.R +5 -0
  88. biopipen/scripts/tcr/Immunarch-diversity.R +25 -4
  89. biopipen/scripts/tcr/Immunarch-geneusage.R +15 -1
  90. biopipen/scripts/tcr/Immunarch-kmer.R +14 -1
  91. biopipen/scripts/tcr/Immunarch-overlap.R +15 -1
  92. biopipen/scripts/tcr/Immunarch-spectratyping.R +10 -1
  93. biopipen/scripts/tcr/Immunarch-tracking.R +6 -0
  94. biopipen/scripts/tcr/Immunarch-vjjunc.R +33 -0
  95. biopipen/scripts/tcr/ScRepLoading.R +127 -0
  96. biopipen/scripts/tcr/TCRClusterStats.R +24 -7
  97. biopipen/scripts/tcr/TCRDock.py +10 -6
  98. biopipen/scripts/tcr/TESSA.R +6 -1
  99. biopipen/scripts/tcr/vdjtools-patch.sh +1 -1
  100. biopipen/scripts/vcf/BcftoolsAnnotate.py +8 -8
  101. biopipen/scripts/vcf/BcftoolsFilter.py +3 -3
  102. biopipen/scripts/vcf/BcftoolsMerge.py +31 -0
  103. biopipen/scripts/vcf/BcftoolsSort.py +4 -4
  104. biopipen/scripts/vcf/BcftoolsView.py +5 -5
  105. biopipen/scripts/vcf/Vcf2Bed.py +2 -2
  106. biopipen/scripts/vcf/VcfAnno.py +11 -11
  107. biopipen/scripts/vcf/VcfDownSample.sh +22 -10
  108. biopipen/scripts/vcf/VcfFilter.py +5 -5
  109. biopipen/scripts/vcf/VcfFix.py +7 -7
  110. biopipen/scripts/vcf/VcfFix_utils.py +12 -3
  111. biopipen/scripts/vcf/VcfIndex.py +3 -3
  112. biopipen/scripts/vcf/VcfIntersect.py +3 -3
  113. biopipen/scripts/vcf/VcfLiftOver.sh +5 -0
  114. biopipen/scripts/vcf/VcfSplitSamples.py +4 -4
  115. biopipen/scripts/vcf/bcftools_utils.py +3 -3
  116. biopipen/scripts/web/Download.py +8 -4
  117. biopipen/scripts/web/DownloadList.py +5 -5
  118. biopipen/scripts/web/GCloudStorageDownloadBucket.py +5 -5
  119. biopipen/scripts/web/GCloudStorageDownloadFile.py +3 -3
  120. biopipen/scripts/web/gcloud_common.py +1 -1
  121. biopipen/utils/gsea.R +96 -42
  122. biopipen/utils/misc.R +205 -7
  123. biopipen/utils/misc.py +17 -8
  124. biopipen/utils/plot.R +53 -17
  125. biopipen/utils/reference.py +11 -11
  126. biopipen/utils/repr.R +146 -0
  127. biopipen/utils/vcf.py +1 -1
  128. {biopipen-0.32.1.dist-info → biopipen-0.33.0.dist-info}/METADATA +9 -9
  129. {biopipen-0.32.1.dist-info → biopipen-0.33.0.dist-info}/RECORD +131 -122
  130. {biopipen-0.32.1.dist-info → biopipen-0.33.0.dist-info}/WHEEL +1 -1
  131. biopipen/scripts/scrna/SeuratClusterStats-hists.R +0 -139
  132. biopipen/scripts/scrna/SeuratPreparing-common.R +0 -452
  133. biopipen/scripts/scrna/SeuratPreparing-doublet_detection.R +0 -201
  134. {biopipen-0.32.1.dist-info → biopipen-0.33.0.dist-info}/entry_points.txt +0 -0

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