biopipen 0.34.4__tar.gz → 0.34.5__tar.gz

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  1. {biopipen-0.34.4 → biopipen-0.34.5}/PKG-INFO +1 -1
  2. biopipen-0.34.5/biopipen/__init__.py +1 -0
  3. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/SeuratClusterStats-features.R +1 -1
  4. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/SeuratClusterStats-stats.R +1 -1
  5. {biopipen-0.34.4 → biopipen-0.34.5}/pyproject.toml +1 -1
  6. {biopipen-0.34.4 → biopipen-0.34.5}/setup.py +1 -1
  7. biopipen-0.34.4/biopipen/__init__.py +0 -1
  8. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/core/__init__.py +0 -0
  9. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/core/config.py +0 -0
  10. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/core/config.toml +0 -0
  11. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/core/defaults.py +0 -0
  12. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/core/filters.py +0 -0
  13. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/core/proc.py +0 -0
  14. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/core/testing.py +0 -0
  15. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/__init__.py +0 -0
  16. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/bam.py +0 -0
  17. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/bed.py +0 -0
  18. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/cellranger.py +0 -0
  19. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/cellranger_pipeline.py +0 -0
  20. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/cnv.py +0 -0
  21. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/cnvkit.py +0 -0
  22. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/cnvkit_pipeline.py +0 -0
  23. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/delim.py +0 -0
  24. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/gene.py +0 -0
  25. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/gsea.py +0 -0
  26. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/misc.py +0 -0
  27. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/plot.py +0 -0
  28. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/protein.py +0 -0
  29. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/regulatory.py +0 -0
  30. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/rnaseq.py +0 -0
  31. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/scrna.py +0 -0
  32. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/scrna_metabolic_landscape.py +0 -0
  33. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/snp.py +0 -0
  34. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/stats.py +0 -0
  35. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/tcgamaf.py +0 -0
  36. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/tcr.py +0 -0
  37. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/vcf.py +0 -0
  38. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/ns/web.py +0 -0
  39. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/bam/CNAClinic.svelte +0 -0
  40. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/bam/CNVpytor.svelte +0 -0
  41. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/bam/ControlFREEC.svelte +0 -0
  42. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/cellranger/CellRangerCount.svelte +0 -0
  43. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/cellranger/CellRangerSummary.svelte +0 -0
  44. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/cellranger/CellRangerVdj.svelte +0 -0
  45. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/cnv/AneuploidyScore.svelte +0 -0
  46. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/cnv/AneuploidyScoreSummary.svelte +0 -0
  47. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/cnv/TMADScoreSummary.svelte +0 -0
  48. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/cnvkit/CNVkitDiagram.svelte +0 -0
  49. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/cnvkit/CNVkitHeatmap.svelte +0 -0
  50. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/cnvkit/CNVkitScatter.svelte +0 -0
  51. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/common.svelte +0 -0
  52. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/gsea/FGSEA.svelte +0 -0
  53. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/gsea/GSEA.svelte +0 -0
  54. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/protein/ProdigySummary.svelte +0 -0
  55. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/scrna/CellsDistribution.svelte +0 -0
  56. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/scrna/DimPlots.svelte +0 -0
  57. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/scrna/MarkersFinder.svelte +0 -0
  58. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/scrna/MetaMarkers.svelte +0 -0
  59. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/scrna/RadarPlots.svelte +0 -0
  60. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte +0 -0
  61. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte +0 -0
  62. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte +0 -0
  63. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/snp/PlinkCallRate.svelte +0 -0
  64. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/snp/PlinkFreq.svelte +0 -0
  65. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/snp/PlinkHWE.svelte +0 -0
  66. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/snp/PlinkHet.svelte +0 -0
  67. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/snp/PlinkIBD.svelte +0 -0
  68. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/tcr/CDR3AAPhyschem.svelte +0 -0
  69. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/tcr/ClonalStats.svelte +0 -0
  70. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/tcr/CloneResidency.svelte +0 -0
  71. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/tcr/Immunarch.svelte +0 -0
  72. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/tcr/SampleDiversity.svelte +0 -0
  73. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/tcr/TCRClusterStats.svelte +0 -0
  74. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/tcr/TESSA.svelte +0 -0
  75. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/tcr/VJUsage.svelte +0 -0
  76. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/utils/misc.liq +0 -0
  77. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/vcf/TruvariBenchSummary.svelte +0 -0
  78. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/reports/vcf/TruvariConsistency.svelte +0 -0
  79. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bam/BamMerge.py +0 -0
  80. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bam/BamSampling.py +0 -0
  81. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bam/BamSort.py +0 -0
  82. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bam/BamSplitChroms.py +0 -0
  83. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bam/BamSubsetByBed.py +0 -0
  84. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bam/CNAClinic.R +0 -0
  85. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bam/CNVpytor.py +0 -0
  86. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bam/ControlFREEC.py +0 -0
  87. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bam/SamtoolsView.py +0 -0
  88. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bed/Bed2Vcf.py +0 -0
  89. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bed/BedConsensus.py +0 -0
  90. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bed/BedLiftOver.sh +0 -0
  91. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bed/BedtoolsIntersect.py +0 -0
  92. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bed/BedtoolsMakeWindows.py +0 -0
  93. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/bed/BedtoolsMerge.py +0 -0
  94. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cellranger/CellRangerCount.py +0 -0
  95. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cellranger/CellRangerSummary.R +0 -0
  96. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cellranger/CellRangerVdj.py +0 -0
  97. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnv/AneuploidyScore.R +0 -0
  98. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnv/AneuploidyScoreSummary.R +0 -0
  99. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnv/TMADScore.R +0 -0
  100. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnv/TMADScoreSummary.R +0 -0
  101. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitAccess.py +0 -0
  102. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitAutobin.py +0 -0
  103. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitBatch.py +0 -0
  104. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitCall.py +0 -0
  105. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitCoverage.py +0 -0
  106. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitDiagram.py +0 -0
  107. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitFix.py +0 -0
  108. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitGuessBaits.py +0 -0
  109. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitHeatmap.py +0 -0
  110. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitReference.py +0 -0
  111. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitScatter.py +0 -0
  112. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/CNVkitSegment.py +0 -0
  113. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/cnvkit/guess_baits.py +0 -0
  114. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/delim/RowsBinder.R +0 -0
  115. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/delim/SampleInfo.R +0 -0
  116. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/gene/GeneNameConversion.R +0 -0
  117. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/gene/GenePromoters.R +0 -0
  118. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/gsea/Enrichr.R +0 -0
  119. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/gsea/FGSEA.R +0 -0
  120. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/gsea/GSEA.R +0 -0
  121. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/gsea/PreRank.R +0 -0
  122. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/misc/Config2File.py +0 -0
  123. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/misc/Plot.R +0 -0
  124. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/misc/Shell.sh +0 -0
  125. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/misc/Str2File.py +0 -0
  126. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/plot/Heatmap.R +0 -0
  127. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/plot/Manhattan.R +0 -0
  128. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/plot/QQPlot.R +0 -0
  129. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/plot/ROC.R +0 -0
  130. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/plot/Scatter.R +0 -0
  131. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/plot/VennDiagram.R +0 -0
  132. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/protein/MMCIF2PDB.py +0 -0
  133. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/protein/PDB2Fasta.py +0 -0
  134. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/protein/Prodigy.py +0 -0
  135. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/protein/ProdigySummary.R +0 -0
  136. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/protein/RMSD.py +0 -0
  137. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/regulatory/MotifAffinityTest.R +0 -0
  138. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/regulatory/MotifAffinityTest_AtSNP.R +0 -0
  139. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/regulatory/MotifAffinityTest_MotifBreakR.R +0 -0
  140. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/regulatory/MotifScan.py +0 -0
  141. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/regulatory/VariantMotifPlot.R +0 -0
  142. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/regulatory/motifs-common.R +0 -0
  143. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/rnaseq/Simulation-ESCO.R +0 -0
  144. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/rnaseq/Simulation-RUVcorr.R +0 -0
  145. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/rnaseq/Simulation.R +0 -0
  146. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/rnaseq/UnitConversion.R +0 -0
  147. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/AnnData2Seurat.R +0 -0
  148. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/CCPlotR-patch.R +0 -0
  149. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/CellCellCommunication.py +0 -0
  150. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/CellCellCommunicationPlots.R +0 -0
  151. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R +0 -0
  152. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/CellTypeAnnotation-direct.R +0 -0
  153. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/CellTypeAnnotation-hitype.R +0 -0
  154. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/CellTypeAnnotation-sccatch.R +0 -0
  155. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/CellTypeAnnotation-sctype.R +0 -0
  156. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/CellTypeAnnotation.R +0 -0
  157. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/CellsDistribution.R +0 -0
  158. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/DimPlots.R +0 -0
  159. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/ExprImputation-alra.R +0 -0
  160. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/ExprImputation-rmagic.R +0 -0
  161. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/ExprImputation-scimpute.R +0 -0
  162. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/ExprImputation.R +0 -0
  163. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/LoomTo10X.R +0 -0
  164. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/MarkersFinder.R +0 -0
  165. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/MetaMarkers.R +0 -0
  166. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/ModuleScoreCalculator.R +0 -0
  167. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/PseudoBulkDEG.R +0 -0
  168. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/RadarPlots.R +0 -0
  169. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/SCImpute.R +0 -0
  170. {biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/ScFGSEA.R +0 -0
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{biopipen-0.34.4 → biopipen-0.34.5}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: biopipen
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- Version: 0.34.4
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+ Version: 0.34.5
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  Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
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  License: MIT
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  Author: pwwang
biopipen-0.34.5/biopipen/__init__.py ADDED
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{biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/SeuratClusterStats-features.R RENAMED
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{biopipen-0.34.4 → biopipen-0.34.5}/biopipen/scripts/scrna/SeuratClusterStats-stats.R RENAMED
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  if (!is.null(case$comparisons)) {
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- "Statistical comparisons were performed between groups using '{case$pairwise_method %||% 'wilcox.test'}' method."
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  [tool.poetry]
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  name = "biopipen"
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- version = "0.34.4"
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+ version = "0.34.5"
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  description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
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  authors = ["pwwang <pwwang@pwwang.com>"]
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  'long_description': 'None',
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  'author': 'pwwang',
biopipen-0.34.4/biopipen/__init__.py DELETED
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- __version__ = "0.34.4"
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