biopipen 0.21.2__py3-none-any.whl → 0.22.1__py3-none-any.whl
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- biopipen/__init__.py +1 -1
- biopipen/core/filters.py +142 -0
- biopipen/ns/scrna.py +19 -1
- biopipen/ns/tcr.py +30 -10
- biopipen/reports/delim/SampleInfo.svelte +2 -22
- biopipen/reports/scrna/CellsDistribution.svelte +4 -39
- biopipen/reports/scrna/MarkersFinder.svelte +6 -126
- biopipen/reports/scrna/MetaMarkers.svelte +3 -75
- biopipen/reports/scrna/RadarPlots.svelte +4 -20
- biopipen/reports/scrna/ScFGSEA.svelte +4 -23
- biopipen/reports/scrna/SeuratClusterStats.svelte +3 -69
- biopipen/reports/scrna/SeuratPreparing.svelte +3 -26
- biopipen/reports/scrna/TopExpressingGenes.svelte +3 -41
- biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte +17 -16
- biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.svelte +13 -16
- biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte +44 -52
- biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte +2 -8
- biopipen/reports/tcr/CDR3AAPhyschem.svelte +18 -65
- biopipen/reports/tcr/CloneResidency.svelte +3 -93
- biopipen/reports/tcr/Immunarch.svelte +4 -168
- biopipen/reports/tcr/TCRClusterStats.svelte +3 -45
- biopipen/reports/tcr/TESSA.svelte +11 -28
- biopipen/scripts/delim/SampleInfo.R +41 -7
- biopipen/scripts/scrna/CellsDistribution.R +127 -16
- biopipen/scripts/scrna/MarkersFinder.R +245 -100
- biopipen/scripts/scrna/MetaMarkers.R +163 -82
- biopipen/scripts/scrna/RadarPlots.R +163 -110
- biopipen/scripts/scrna/ScFGSEA.R +51 -11
- biopipen/scripts/scrna/SeuratClusterStats-dimplots.R +26 -13
- biopipen/scripts/scrna/SeuratClusterStats-features.R +58 -53
- biopipen/scripts/scrna/SeuratClusterStats-stats.R +39 -21
- biopipen/scripts/scrna/SeuratClusterStats.R +4 -2
- biopipen/scripts/scrna/SeuratClustering.R +73 -26
- biopipen/scripts/scrna/SeuratMetadataMutater.R +13 -1
- biopipen/scripts/scrna/SeuratPreparing.R +93 -19
- biopipen/scripts/scrna/TopExpressingGenes.R +100 -18
- biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R +21 -8
- biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R +25 -3
- biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R +1 -0
- biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R +14 -3
- biopipen/scripts/tcr/Attach2Seurat.R +2 -1
- biopipen/scripts/tcr/CDR3AAPhyschem.R +123 -10
- biopipen/scripts/tcr/CloneResidency.R +114 -34
- biopipen/scripts/tcr/Immunarch-basic.R +18 -4
- biopipen/scripts/tcr/Immunarch-clonality.R +14 -0
- biopipen/scripts/tcr/Immunarch-diversity.R +123 -18
- biopipen/scripts/tcr/Immunarch-geneusage.R +23 -1
- biopipen/scripts/tcr/Immunarch-kmer.R +45 -3
- biopipen/scripts/tcr/Immunarch-overlap.R +62 -0
- biopipen/scripts/tcr/Immunarch-spectratyping.R +18 -2
- biopipen/scripts/tcr/Immunarch-tracking.R +24 -1
- biopipen/scripts/tcr/Immunarch-vjjunc.R +17 -2
- biopipen/scripts/tcr/Immunarch.R +7 -0
- biopipen/scripts/tcr/ImmunarchLoading.R +22 -23
- biopipen/scripts/tcr/TCRClusterStats.R +124 -11
- biopipen/scripts/tcr/TCRClustering.R +8 -9
- biopipen/scripts/tcr/TESSA.R +66 -41
- biopipen/utils/misc.R +96 -1
- {biopipen-0.21.2.dist-info → biopipen-0.22.1.dist-info}/METADATA +1 -1
- {biopipen-0.21.2.dist-info → biopipen-0.22.1.dist-info}/RECORD +62 -62
- {biopipen-0.21.2.dist-info → biopipen-0.22.1.dist-info}/WHEEL +0 -0
- {biopipen-0.21.2.dist-info → biopipen-0.22.1.dist-info}/entry_points.txt +0 -0
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