biopipen 0.31.6__py3-none-any.whl → 0.32.0__py3-none-any.whl

{biopipen-0.31.6.dist-info → biopipen-0.32.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=KU7MsdICtcB5jVm5DAaNainBCUqYItaZLSuj12ONgkE,23
+biopipen/__init__.py,sha256=s1FApnNsg-mmWP3shY6ep6EAjZrNFXHlyBXWcP2KV6Q,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=7IXvviRicZ2D1h6x3BVgbLJ96nsh-ikvZ0sVlQepqFE,1944
@@ -7,8 +7,8 @@ biopipen/core/filters.py,sha256=5bZsbpdW7DCxqiteRdb2gelmXvfqWPmPsFxrpHdWsoE,1298
 biopipen/core/proc.py,sha256=60lUP3PcUAaKbDETo9N5PEIoeOYrLgcSmuytmrhcx8g,912
 biopipen/core/testing.py,sha256=lZ_R5ZbYPO2NPuLHdbzg6HbD_f4j8paVVbyeUqwg6FE,3411
 biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biopipen/ns/bam.py,sha256=-xVagotsURyOtwKzv72L-2f9P7467OVzgvP96syfHZc,10628
-biopipen/ns/bed.py,sha256=HsTCJge7XNfCZyCBJ4iifNKQ5we4VZSpRx8XL8--y5A,6689
+biopipen/ns/bam.py,sha256=OtvzEadx-zpr98PoZoozbQszcQBvtFDMuAtuwH-3JUw,11394
+biopipen/ns/bed.py,sha256=EqpSa7Hx6GImvJNghtV4uDo2PnPXeUt1Yq9AFWJP9_8,8159
 biopipen/ns/cellranger.py,sha256=yPBoNzVSY74J7uyVucaob5lqZKKru5-hYSM4f4Nr2OY,5553
 biopipen/ns/cellranger_pipeline.py,sha256=EWkPJTujamNSMQoRnKfhUiIj6TkMfRmCSUbPfd8Tv8E,4011
 biopipen/ns/cnv.py,sha256=ssQAHf2MB675avoXVRkYy0vGiqIpRpRExywjhbymmBI,7811
@@ -22,7 +22,7 @@ biopipen/ns/plot.py,sha256=XzLq0A8qCIQRbxhPEdWhEfbRZ8g3e4KriVz0RP8enNY,18078
 biopipen/ns/protein.py,sha256=33pzM-gvBTw0jH60mvfqnriM6uw2zj3katZ82nC9owI,3309
 biopipen/ns/regulatory.py,sha256=gJjGVpJrdv-rg2t5UjK4AGuvtLNymaNYNvoD8PhlbvE,15929
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=fXP_h7gchcuk_Jwos0IgY_P8ON6Q995OgKHgdrxfvAY,112868
+biopipen/ns/scrna.py,sha256=viIfqTH_0f7kSpHpKfrUf7HUr_w-V_oRYRj1TwuXYNs,120878
 biopipen/ns/scrna_metabolic_landscape.py,sha256=6AhaynGG3lNRi96N2tReVT46BJMuEwooSSd2irBoN80,28347
 biopipen/ns/snp.py,sha256=-Jx5Hsv_7KV7TqLU0nHCaPkMEN0CFdi4tNVlyq0rUZ4,27259
 biopipen/ns/stats.py,sha256=DlPyK5Vsg6ZEkV9SDS3aAw21eXzvOHgqeZDkXPhg7go,20509
@@ -46,6 +46,7 @@ biopipen/reports/delim/SampleInfo.svelte,sha256=Vpjrdd3AXNDNhx2pzDaFA61xPMYAFKvv
 biopipen/reports/gsea/FGSEA.svelte,sha256=3gNbZovmRWK6QjtxfgZgmft6LUurVZfQyHBRqyGMosk,405
 biopipen/reports/gsea/GSEA.svelte,sha256=lYHf8h8RLx3i-jNCEGu_LM-dbYm9ZJDzyAEadsZXzmQ,417
 biopipen/reports/protein/ProdigySummary.svelte,sha256=WEYPwmcmgtSqpFpTvNPV40yZR-7ERa5LgZni2RXxUZQ,348
+biopipen/reports/scrna/CellCellCommunicationPlots.svelte,sha256=McLQtgzbJGnb9o3GC17sRee96e-naPNPIF8SQyRp-Kc,346
 biopipen/reports/scrna/CellsDistribution.svelte,sha256=Mg6P0tazpzOxsOAtc-0LGEim5KprPt5KIgoW3TzrxxA,413
 biopipen/reports/scrna/DimPlots.svelte,sha256=ZLbtN0ioevRyEky4jb_DkDGAcpy_jAhaHfFym5ELEPM,479
 biopipen/reports/scrna/MarkersFinder.svelte,sha256=77rD1psj0VJykPDhfwS-B8mubvaasREAE6RYR2atTN4,444
@@ -53,7 +54,7 @@ biopipen/reports/scrna/MetaMarkers.svelte,sha256=iIFRKjvVYrM1AtDWqq8UfeS8q23R8FK
 biopipen/reports/scrna/RadarPlots.svelte,sha256=g_fp9d3vdnzk-egXPhkhhfWXOeG569Rj8rYLRIKmlLc,396
 biopipen/reports/scrna/ScFGSEA.svelte,sha256=Gqt-XjqsB3XgdR3XukvphwyMExZpScwqgEo7AD-gK6g,491
 biopipen/reports/scrna/SeuratClusterStats.svelte,sha256=rTsoOCiVm7lEyBYgu2ZVcKNGi4g6PynYoOSx0DHdTHo,429
-biopipen/reports/scrna/SeuratMap2Ref.svelte,sha256=SYuoKJR1PuBf9c7WvUXXjmokVo-JxFLqZqiu9kTtLuY,542
+biopipen/reports/scrna/SeuratMap2Ref.svelte,sha256=1g-FEmvR2YMn0OF66qESNBWmGdHQY3u8QuG4M-T7Y4E,659
 biopipen/reports/scrna/SeuratPreparing.svelte,sha256=CCQ3qodjfoQeMZhSZp7irvSqBt10m7urzcWEOHsZa8M,365
 biopipen/reports/scrna/TopExpressingGenes.svelte,sha256=h2Or2cKCzuY2cypq1PKrqiHFVMZmFUgFOXoQumvfGSk,471
 biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=4M8V6jDv1_ZviTsRdoYNQixoTnKiD06oPHzVabUTq6k,978
@@ -79,6 +80,7 @@ biopipen/reports/vcf/TruvariConsistency.svelte,sha256=BBvtxi1EPmGH7j5M5zMOcLEhKW
 biopipen/scripts/bam/BamMerge.py,sha256=Gd5P8V-CSsTAA8ZrUxetR-I49GjJ3VJNjrqu7-EZwXQ,3642
 biopipen/scripts/bam/BamSampling.py,sha256=Pi6CXAbBFVRGh8-0WrkB-3v3oxinfahQk11H0IdBNmQ,2312
 biopipen/scripts/bam/BamSplitChroms.py,sha256=b7GS2I4X0dLOhlPg_r9-buoIHTWlq6zHI3Rox94LXR8,4893
+biopipen/scripts/bam/BamSubsetByBed.py,sha256=QpY6WDJfbO3k2FdMyfgstFKgTdtOc1beGoUF5FI5EAc,1027
 biopipen/scripts/bam/CNAClinic.R,sha256=mQXwtShL54HZXGCPqgPKPrU74_6K_8PqtOtG0mgA-F0,5062
 biopipen/scripts/bam/CNVpytor.py,sha256=hOUli9BDMOoth0or-tjUYC1AP3yNOuxUS6G3Rhcg99s,18000
 biopipen/scripts/bam/ControlFREEC.py,sha256=oX6iWsos-CfiT_ViDBrKeMOOIVdCKWrB-_MqzLgEF9s,3267
@@ -86,6 +88,7 @@ biopipen/scripts/bed/Bed2Vcf.py,sha256=u0mp_2Y4UtEA839zq9UENesH6Gyiwd4sZQW9wFnBV
 biopipen/scripts/bed/BedConsensus.py,sha256=gfAxuIalvCEpS0tiOyAJGPYGgHN0L-hm0K37Iteh5yw,2386
 biopipen/scripts/bed/BedLiftOver.sh,sha256=Y4gBsz9w4zhE29UmWojO6F4PXMMMWC1uCzjrxa19eOs,256
 biopipen/scripts/bed/BedtoolsIntersect.py,sha256=sFyXPL3kG59xa5eJwHumcQLw3lfabOXsq2-k8IgIqt4,1722
+biopipen/scripts/bed/BedtoolsMakeWindows.py,sha256=Ip4U0ORXti65g7znZeHEbvw2PGlCxoEfeucZmw4wb1o,1428
 biopipen/scripts/bed/BedtoolsMerge.py,sha256=7mt307V_wWa_ME0VfuMsVX0HgEwfDcZtY_bDvOPjFiQ,368
 biopipen/scripts/cellranger/CellRangerCount.py,sha256=b9kkHPpq-bFh-3XCUdxdMKg3SsZmEzZFrG3dbtb4fX8,2875
 biopipen/scripts/cellranger/CellRangerSummary.R,sha256=mVOCIHngEpJIKVD3tMG5UWqS0OQGGjY6yx6ikRcqQU4,11067
@@ -136,7 +139,10 @@ biopipen/scripts/rnaseq/Simulation-ESCO.R,sha256=68cEHDdJclX8P8Q7ey9yBOfK09M_kxl
 biopipen/scripts/rnaseq/Simulation-RUVcorr.R,sha256=6C6Ke5RLF0fC2V9WQPoFEdqoDabCnhslZBIyB6zhIxc,1155
 biopipen/scripts/rnaseq/Simulation.R,sha256=PK9tZS88AcBPStcFalZlMU0KE0gSqFSQvhUoQ-8eg90,871
 biopipen/scripts/rnaseq/UnitConversion.R,sha256=pr1uZuzjapZKwIupE-xtE2HW-OwdVCGBVaHQ_3ipIDw,11377
-biopipen/scripts/scrna/AnnData2Seurat.R,sha256=8VEXHnknoEPWRQ0cj80so6O5FAd1_YlwQ0CP0TwmZVo,2555
+biopipen/scripts/scrna/AnnData2Seurat.R,sha256=PohvXtUziu0_A_HL5HaOYG1wSVdLgMaV8yhzEKDQT84,2814
+biopipen/scripts/scrna/CCPlotR-patch.R,sha256=KpB8fwacBaWaUNjIidcLUkMShLjS4Gq9UY8LUgIITB0,8369
+biopipen/scripts/scrna/CellCellCommunication.py,sha256=1txufcxFsniB9UET_L2RA2qaQZfjidjUbUsese_hoGE,2899
+biopipen/scripts/scrna/CellCellCommunicationPlots.R,sha256=KE-yy7TkMjPz4opfQgosr6NfMQQYeg4mgzfDod-RJrQ,6104
 biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R,sha256=2lkIwtSw2A21RCUBdo3BVUdAwsLTIq65NDA-ZR1YWE0,9644
 biopipen/scripts/scrna/CellTypeAnnotation-common.R,sha256=s2exGdJ3WM8mDDeBXGUxuKO1DAGVgRiirHaJD0lPgDw,336
 biopipen/scripts/scrna/CellTypeAnnotation-direct.R,sha256=hmuk3G4IbF66Sv4RmrcrKn8b4J7ZEBD5PzJHa5EKYB8,2125
@@ -157,7 +163,7 @@ biopipen/scripts/scrna/RadarPlots.R,sha256=4zs0hAm7yq1Ls62f_29koPLqAKCeKbYiztNM-
 biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
 biopipen/scripts/scrna/ScFGSEA.R,sha256=MFoJ3i3LFBfsPCxwLPnTh141ZJyrzwnrTuCZIFwvYjU,6318
 biopipen/scripts/scrna/ScSimulation.R,sha256=b2LtL68ucxLoI57tSEDD0hOSbVHUA_x88Y96eK07N-s,1712
-biopipen/scripts/scrna/Seurat2AnnData.R,sha256=G7bcHGffdNlz6Uuy98tQdlahXiPkTDokflp1yTUgcSQ,1578
+biopipen/scripts/scrna/Seurat2AnnData.R,sha256=zXkdHEqv6H8RCw1bEPStvYHVpu5oRnioWxz164MgHxQ,276
 biopipen/scripts/scrna/SeuratClusterStats-clustree.R,sha256=FkbniQMHiZGrFAIuS8nUfPVJKFofSL-ZnpxTqIhTa54,3058
 biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=NEdlJHNXnJZfF7YkefYVWTPO8Z_KAppRAs9rNvB8TXs,2360
 biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=DeGo7AkBRq0V3Y3JDaifId6rrr5dwawTzcSAJ3W1lxE,15614
@@ -169,7 +175,7 @@ biopipen/scripts/scrna/SeuratClustering-common.R,sha256=JX4Cn2FC6GOcBqaVyGDD3MM5
 biopipen/scripts/scrna/SeuratClustering.R,sha256=0OKRBQ5rFuupK7c03_sSt2HMwMdMnCYFqTvkRXFKchs,1706
 biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zykkJtg2lM,509
 biopipen/scripts/scrna/SeuratLoading.R,sha256=ekWKnHIqtQb3kHVQiVymAHXXqiUxs6KKefjZKjaykmk,900
-biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=B0RZ2k1IUKdhe34SjU-8CxvYGj7ub-z7JJaSE0snCok,12040
+biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=MP6ttYv8bK5kzWNoP3DXEad06snotVOqCqdvBHsOasc,12776
 biopipen/scripts/scrna/SeuratMetadataMutater.R,sha256=PMwG0Xvl_EEVKkicfrIi4arEqpY948PkYLkb59kTAXI,1135
 biopipen/scripts/scrna/SeuratPreparing-common.R,sha256=WuD7lGS17eAUQWSiIdAoV0EIeqS3Tnkkx-7PbP6Q3tc,16279
 biopipen/scripts/scrna/SeuratPreparing-doublet_detection.R,sha256=TNN2lfFjpnnO0rguMsG38JYCP1nFUhcPLJ1LqGj-Sc8,6674
@@ -210,10 +216,10 @@ biopipen/scripts/tcr/Attach2Seurat.R,sha256=0KZaBkuPvqOBXq4ZG3pzIIua5HL-161K5dVX
 biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=ZxHyn4vJF-1PDbnbozovOipET_QZKqeFrKUibRpLgzw,16825
 biopipen/scripts/tcr/CloneResidency.R,sha256=KAcFB39vTYsk8IEj44s8oSFVhKjpAdJ8hkpKxtdWzRA,21540
 biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=hds1C80Q_W40Ikp-BrFfvh_aBf_V61lz-1YAvkDESyk,4569
-biopipen/scripts/tcr/GIANA/GIANA.py,sha256=0qLhgCWxT8K-4JvORA03CzBPTT5pd4Di5B_DgrHXbFA,47198
-biopipen/scripts/tcr/GIANA/GIANA4.py,sha256=Z7Q3cUr1Pvmy4CFADN0P7i9g1-HbzWROMqk5HvL_F1Q,45762
+biopipen/scripts/tcr/GIANA/GIANA.py,sha256=jo0d58K57CF4W6mc2Q-hQn9rLl6oLHTsr5JceP8xqN0,54874
+biopipen/scripts/tcr/GIANA/GIANA4.py,sha256=X_iXdgKZ9V5T87jXBdml0H6bwiDjsAqoPKhsdF72lj8,53904
 biopipen/scripts/tcr/GIANA/Imgt_Human_TRBV.fasta,sha256=XUwDPXJxVH5O9Q0gCL6EILKXEwVyiAZXm4VS2vkPcnQ,15371
-biopipen/scripts/tcr/GIANA/query.py,sha256=5NWSEDNrJomMt48tzLGpRwJTZB0zQxvMVTilyG8osX8,7298
+biopipen/scripts/tcr/GIANA/query.py,sha256=YJeCk24Hab7XfQxZ5VNesdjr_LVxPH0KH9rwGm1ePf4,7680
 biopipen/scripts/tcr/Immunarch-basic.R,sha256=2UAQtGEDKgf5LmPeGlNkkAfQOCtdYpCiBMAn-JHOV4A,3036
 biopipen/scripts/tcr/Immunarch-clonality.R,sha256=NN6WikD-9BKodgKRAbvM2oMLrhn9FUWjqIb69DpHnAk,3744
 biopipen/scripts/tcr/Immunarch-diversity.R,sha256=6T8-IXIMyy4YXgIA4TXJThy91FqgLVsljqxd3PxLDys,27136
@@ -230,7 +236,7 @@ biopipen/scripts/tcr/ImmunarchLoading.R,sha256=Vw2oIza3mDJzg9kuo-w5jvwdivk4AtDA6
 biopipen/scripts/tcr/ImmunarchSplitIdents.R,sha256=FGCeGV0uSmFU91lKkldUAeV4A2m3hHw5X4GNi8ffGzI,1873
 biopipen/scripts/tcr/SampleDiversity.R,sha256=oipN4-2nQZe8bYjI0lZ0SvZ7T8GZ_FWkpkobi1cwmWE,2664
 biopipen/scripts/tcr/TCRClusterStats.R,sha256=QhXgfKSh27VHO901hDizyGYTXMYFJxW22StchQUq3uE,12906
-biopipen/scripts/tcr/TCRClustering.R,sha256=MRCaFbgMhhW9uimVBrE1Q5VqqxQpnKv5W2ILWmHdkU8,9593
+biopipen/scripts/tcr/TCRClustering.R,sha256=Lt_e32c52gJ9fz1abboGXLIR--Lx2dqW0oFlSOCrCVs,10079
 biopipen/scripts/tcr/TCRDock.py,sha256=jjzxMWp-hs0LDtA1mVbiWDvUieSO7X-F9yeKGy1LSTM,3026
 biopipen/scripts/tcr/TESSA.R,sha256=XFC2P_e_Gm83jG5EjzVIW6KcyG5IieAaK7sXDA3_oZ0,6864
 biopipen/scripts/tcr/TESSA_source/Atchley_factors.csv,sha256=SumqDOqP67P54uM7Cuc5_O_rySTWcGo7eX3psMSPX9s,763
@@ -282,9 +288,9 @@ biopipen/utils/mutate_helpers.R,sha256=Bqy6Oi4rrPEPJw0Jq32bVAwwBfZv7JJL9jFcK5x-c
 biopipen/utils/plot.R,sha256=fmWnCv6EpOU8NvHFvShbdPRqB659vHcDlJAqWIXM8XQ,4415
 biopipen/utils/reference.py,sha256=oi5evicLwHxF0KAIPNZohBeHJLJQNWFJH0cr2y5pgcg,5873
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
-biopipen/utils/single_cell.R,sha256=pJjYP8bIZpNAtTQ32rOXhZxaM1Y-6D-xUcK3pql9tbk,4316
+biopipen/utils/single_cell.R,sha256=3jmTV9-kHTXyBA6GRlRf_Ig0jx_5jRr6E1THoa1869k,7564
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.31.6.dist-info/METADATA,sha256=2NGpF5QMNq7lG0y8MQIGpfFYyRE9lYz17RpF6dEtq0k,882
-biopipen-0.31.6.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-biopipen-0.31.6.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
-biopipen-0.31.6.dist-info/RECORD,,
+biopipen-0.32.0.dist-info/METADATA,sha256=1kWhdtPEVLqTrBh-9eK1I-Fb7KVCycmWJTA4_HXQLlw,882
+biopipen-0.32.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+biopipen-0.32.0.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
+biopipen-0.32.0.dist-info/RECORD,,