biopipen 0.34.1__py3-none-any.whl → 0.34.3__py3-none-any.whl

{biopipen-0.34.1.dist-info → biopipen-0.34.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=Z-DRdi7fjebiPt8V6ExiicJOI_-UPpu6i21-wLM1PPE,23
+biopipen/__init__.py,sha256=9zEyyJeo61cIb6C5CZbqmNlJcQECUf2x7wa5gC31VGY,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=lZV_vbYWk6uqm19ZWJcsZCcSNqAdIfN2fOfamzxZpg4,2148
@@ -22,12 +22,12 @@ biopipen/ns/plot.py,sha256=N41_izb6zi-XArUly5WhLebapNXbTNSgGlOCCwtrDlY,18282
 biopipen/ns/protein.py,sha256=YJtlKoHI2p5yHdxKeQnNtm5QrbxDGOq1UXOdt_7tlTs,6391
 biopipen/ns/regulatory.py,sha256=gJjGVpJrdv-rg2t5UjK4AGuvtLNymaNYNvoD8PhlbvE,15929
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=cxEVHGgHF7id3eegVQLOZWwuG0iMSlP4ZnZ9nizw7ac,131196
-biopipen/ns/scrna_metabolic_landscape.py,sha256=Q95KkHg5jC6eUMSUH-wioPxOzuArP59j3CPsfDTCBM0,22096
+biopipen/ns/scrna.py,sha256=BqPcyILaLWYEg-RT8olKQJPqkF8ILPIMT_BvZZ_Jm5w,144748
+biopipen/ns/scrna_metabolic_landscape.py,sha256=EwLMrsj_pTqvyAgtHLoishjQxCg_j8n5OofuTofUph0,22096
 biopipen/ns/snp.py,sha256=iXWrw7Lmhf4_ct57HGT7JGTClCXUD4sZ2FzOgsC2pTg,28123
 biopipen/ns/stats.py,sha256=DlPyK5Vsg6ZEkV9SDS3aAw21eXzvOHgqeZDkXPhg7go,20509
 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
-biopipen/ns/tcr.py,sha256=Gzoz2FIFmeq_--6ppKVt26kjnPHnWHWAzdj1YvBhrRk,99036
+biopipen/ns/tcr.py,sha256=urx0RomtzhyEtE0V8r3mpNUEMSZCXJ8T6C_I1TSShSY,99373
 biopipen/ns/vcf.py,sha256=zjOH2qiSJsHACLmBqV-Tew-mn-peZgvYLAWjTLh7uTI,23823
 biopipen/ns/web.py,sha256=8VY4Xsb8UrzS4IkGUX_84GQP1JG6NcTZrV7f9tA1tUI,5458
 biopipen/reports/bam/CNAClinic.svelte,sha256=D4IxQcgDCPQZMbXog-aZP5iJEQTK2N4i0C60e_iXyfs,213
@@ -51,10 +51,9 @@ biopipen/reports/scrna/DimPlots.svelte,sha256=ubIx8dgppzSB8WS_B4LN2T3bOTerP4Ck6o
 biopipen/reports/scrna/MarkersFinder.svelte,sha256=77rD1psj0VJykPDhfwS-B8mubvaasREAE6RYR2atTN4,444
 biopipen/reports/scrna/MetaMarkers.svelte,sha256=iIFRKjvVYrM1AtDWqq8UfeS8q23R8FKg2yepKAw2KSE,508
 biopipen/reports/scrna/RadarPlots.svelte,sha256=g_fp9d3vdnzk-egXPhkhhfWXOeG569Rj8rYLRIKmlLc,396
-biopipen/reports/scrna/TopExpressingGenes.svelte,sha256=tt5_Vjym4coFT8Bvz0s6ZcCioTOIwCj83jdCGqPCmUw,491
-biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=1RC-FuYr_M1xInPaNrEGyzPQGy2d1rZjYdKPfLAOPUs,2346
-biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=VTU-D8iELO7zzK5cJg7oZTna2wu4O_gJ8d7G8N7Veg8,5473
-biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte,sha256=Fr9_DJPuv2hzac-zzqtVBir-FXwN-g2fyi7Le_7xfPs,2828
+biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=0AmtzoGZXh5OnxGtZd5NBItVd-BeuGk9mEIhhWa1ab8,2527
+biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=RpIT1O3yiJEEqRcdS-ydYDghChQ0YLbD1RtSK2CQS_k,5654
+biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte,sha256=kW6AxFr7VnX9yVL74IbUEBuI7xRfbmnROXR6C7jRets,3009
 biopipen/reports/snp/PlinkCallRate.svelte,sha256=u0JGUzBS6MJR38TrI7tz08E7uFJToFPeALinu-KLUOg,706
 biopipen/reports/snp/PlinkFreq.svelte,sha256=GCLQXL3OY4b8BDzaLZ3vHVrsv2lNm5657UaSdiimE9w,523
 biopipen/reports/snp/PlinkHWE.svelte,sha256=zlAbn0DLwGBka-X9-MQplpfYkQIanH-QhgQL2GtK0UA,490
@@ -143,7 +142,7 @@ biopipen/scripts/scrna/AnnData2Seurat.R,sha256=wc5PDbK9TkuJtoXXxF4W1ODylWhyfKWd3
 biopipen/scripts/scrna/CCPlotR-patch.R,sha256=KpB8fwacBaWaUNjIidcLUkMShLjS4Gq9UY8LUgIITB0,8369
 biopipen/scripts/scrna/CellCellCommunication.py,sha256=Wg0uFSo0Yt0wq6UT1TBodyK8GtWQXGv7hXRfM665paU,4354
 biopipen/scripts/scrna/CellCellCommunicationPlots.R,sha256=4l2EJVd1y94Nfry8fuRL9OSF6AhS8PGBekimpRUu3s8,1919
-biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R,sha256=mq1Qi90d_8oyoYT4UONm3Dj3aPxikFghfDSLocE9g4k,7169
+biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R,sha256=AlNx0vBKqvpQ83yfNUbU4taJ8CUyz63iXzumZcw-PBc,6968
 biopipen/scripts/scrna/CellTypeAnnotation-direct.R,sha256=w3CKRUA9NZfC3TFbU8I35L4XJ6MtVaWX-VnV7ScZlBI,2196
 biopipen/scripts/scrna/CellTypeAnnotation-hitype.R,sha256=vvjhxin4aoA9heecey0dpr6ofirybygY3ApjgtQW89Y,2094
 biopipen/scripts/scrna/CellTypeAnnotation-sccatch.R,sha256=xxB4K1MzBSNQnDxa44s5ExeU67MbncOBf8lGFr7RvwQ,1870
@@ -156,22 +155,22 @@ biopipen/scripts/scrna/ExprImputation-rmagic.R,sha256=ePgbMZ_3bKbeUrjsMdkdtBM_MS
 biopipen/scripts/scrna/ExprImputation-scimpute.R,sha256=MI_bYfvCDKJsuGntUxfx_-NdrssBoQgL95-DGwJVE5s,1191
 biopipen/scripts/scrna/ExprImputation.R,sha256=GcdZJpkDpq88hRQjtLZY5-byp8V43stEFm5T-pQbU6A,319
 biopipen/scripts/scrna/LoomTo10X.R,sha256=c6F0p1udsL5UOlb84-53K5BsjSDWkdFyYTt5NQmlIec,1059
-biopipen/scripts/scrna/MarkersFinder.R,sha256=eg7_z5Q2qZ_AeGhyo0WyM42QUzsHmJ5TV3hh7PFmHZg,23807
+biopipen/scripts/scrna/MarkersFinder.R,sha256=P6BgseCrXTeJR8X52hzD16qBUuCeHmPc96h5pKE_-qY,24207
 biopipen/scripts/scrna/MetaMarkers.R,sha256=BgYaWYEj6obwqaZaDWqNPtxb1IEEAnXAeBE0Ji9PvBA,12426
 biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=-tByCPk7i070LynAb0z2ANeRxr1QqiKP0dfrJm52jH4,4198
+biopipen/scripts/scrna/PseudoBulkDEG.R,sha256=32Hd3x2WyTFv175Os4bxf6goAcIq7QN8m1i7i7emnMI,22308
 biopipen/scripts/scrna/RadarPlots.R,sha256=Kn1E-hpczuujpgNjR8MqeIIVN-S3PbpmfcKWGKcNCVY,14546
 biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
-biopipen/scripts/scrna/SCP-plot.R,sha256=QcR2zOjRlSA_z4L8l89FWPU7TGxpXlKUe4kPdZU9MuY,787291
-biopipen/scripts/scrna/ScFGSEA.R,sha256=St81BfGi7pGX-y5Lsix7o0Bs2Fv_DKb1rHPXBADEa_8,11459
+biopipen/scripts/scrna/ScFGSEA.R,sha256=Cbr1RE4jD3CbR7K4Y1XWKfcqiqhZmzATCKEd3ysCnCc,11517
 biopipen/scripts/scrna/ScSimulation.R,sha256=q0-dXD9px1cApc_TxGmR-OdNHE8W1VSVWfSI57B96bo,1697
 biopipen/scripts/scrna/ScVelo.py,sha256=SPUZFgZW1Zhw-bnjJo98RK0vpuNFODQ8Q3eTguNc84k,21359
 biopipen/scripts/scrna/Seurat2AnnData.R,sha256=F8g5n2CqX4-KBggxd8ittz8TejYuqqNLMudAHdFt1QM,184
-biopipen/scripts/scrna/SeuratClusterStats-clustree.R,sha256=QmNJicjbLIXYg_RduXHGboCzPEqcFXq32flk5XAqQBg,2886
-biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=tCf3BVoXroeGuMcix8BiB1CA7wUpirBow4T6P3HM02k,1541
-biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=vFLTzF4hje-7JXy-hYxCZgsasbVByvVkqrTFlxzMTB0,5307
+biopipen/scripts/scrna/SeuratClusterStats-clustree.R,sha256=K2pRNe3qFjTJY3VL4EQFxoU1Lzp5DUavhcfx6HZk2J8,3954
+biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=2YNUxPz1xwND9yrOtBZ75u-wwnmkJUkoUyeBlJvBWKQ,1541
+biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=s_NjsK9YNF-POnzIiavG3RrKd9dihxR9ic8kVOSSZfI,7312
 biopipen/scripts/scrna/SeuratClusterStats-ngenes.R,sha256=BN8HSl1HoZp8ibESaCVEJPCBWzmu1AFLMgW5ZeZphS0,3077
-biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=u8KOeWLDk7i-ZGGcgZPyNqmchkrePdKq5JLrl4ZCCT8,2297
-biopipen/scripts/scrna/SeuratClusterStats.R,sha256=lQfl97ARx_l8YNJ1rEdaU-G6EIS-mbFf2rtWLaA6unE,1824
+biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=iRzuv6s_jD4vmheTSEsqp1Q8OQanmxvQoCkrnHQ0hfg,3590
+biopipen/scripts/scrna/SeuratClusterStats.R,sha256=ITFqh7p1ggtDXzVxbBEO2TcdOw4dA6oGhL5m7hFAQmU,1838
 biopipen/scripts/scrna/SeuratClustering.R,sha256=W9HI3Fk3u8MVNycffip8LYRnGg7pW07io7YbtfSk2Pw,979
 biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zykkJtg2lM,509
 biopipen/scripts/scrna/SeuratLoading.R,sha256=23KAgsj0-XZhOOdUlLrb3r17St4LzZq230UlfIjLn_E,892
@@ -184,13 +183,13 @@ biopipen/scripts/scrna/SeuratSubset.R,sha256=yVA11NVE2FSSw-DhxQcJRapns0tNNHdyDYi
 biopipen/scripts/scrna/SeuratTo10X.R,sha256=1mh1R0Qlo1iHVrpMLUXyLDOA92QKJ4GzTMURTFRqsWg,901
 biopipen/scripts/scrna/Slingshot.R,sha256=wo1zq2Wl6u1HODNzZGjjQLcqKeh9sh7FXPs_iKu6tqw,1750
 biopipen/scripts/scrna/Subset10X.R,sha256=dT1QY5mHaDcqOMgAtTfyU1FRBNFtfg3nMGCubvBJcSQ,2671
-biopipen/scripts/scrna/TopExpressingGenes.R,sha256=K6p7Fac_-4GXCI_TyoLxlTaCaX11DzOihfJ6_Yrs3yk,6869
-biopipen/scripts/scrna/celltypist-wrapper.py,sha256=upyh035IqDHxljbTaoXwdDmctcx-fDwN56kGvC2xsbw,1776
+biopipen/scripts/scrna/TopExpressingGenes.R,sha256=9xXx7U6ZLNeZslqhYuxWYQJmgUsTD3qXFew-7zYCJu8,6910
+biopipen/scripts/scrna/celltypist-wrapper.py,sha256=UMCPCpH4MhAvAAtw_HQKac5NlmEW4cwcy_5O6NG4sIo,1919
 biopipen/scripts/scrna/sctype.R,sha256=NaUJkABwF5G1UVm1CCtcMbwLSj94Mo24mbYCKFqo1Bw,6524
 biopipen/scripts/scrna/seurat_anndata_conversion.py,sha256=Ya0Wn2TLg1j66N41PdiXXGE8LtE51eC8XnkGi_q2ey8,2437
-biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=r67kPatUdJeVO_qi7nUrPjplOMuzr7h6r1zScINamtQ,17534
-biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=mQ6h6DsdfsIRzcM_vUaZ_4vayLbNYA_m6wE5vIPzDEo,19454
-biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=64vV9vYnwh93-t6mVvPJDekd9wA_xyMG7K0RRM2e7XQ,9033
+biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=ybgUpjex2VHS4aqPMJdNMw4pV305PctGXjGmzdVLMgI,17822
+biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=fUIibKV-zqqm-ppjUlTY4eq7zNPACmUG8OZ2n48VnBA,19462
+biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=Kd60fZsC1IBQ3hYN4LjofWpJmY-CoXh1veNQvOGAiqs,9127
 biopipen/scripts/snp/MatrixEQTL.R,sha256=Jzb4nYWJJHMsYNbAnyW8rzD4u_EYzFbVxIl80ZHRAbs,7863
 biopipen/scripts/snp/Plink2GTMat.py,sha256=pqFxZgJJ0qcdb3alU8tglsFmBZPNPEXeRWOxrKp790Y,5583
 biopipen/scripts/snp/PlinkCallRate.R,sha256=fKPTwumVnR5xZjJiuwryMaUOl3Vnbb__EinQjobsums,5961
@@ -217,7 +216,7 @@ biopipen/scripts/tcr/ClonalStats.R,sha256=skqPMTHL8zMGIZ2Q_gKXm9UDFRR-wFRurtrmvb
 biopipen/scripts/tcr/CloneResidency.R,sha256=3pong__cdn2bW7pctq4TLcEdcj_xNigzyKnznnmc1i8,22021
 biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=zw5WPgq_lbfdDb9Ou07boh9D2FYjXZtCQKZCP0PKMYw,4561
 biopipen/scripts/tcr/GIANA/GIANA.py,sha256=jo0d58K57CF4W6mc2Q-hQn9rLl6oLHTsr5JceP8xqN0,54874
-biopipen/scripts/tcr/GIANA/GIANA4.py,sha256=X_iXdgKZ9V5T87jXBdml0H6bwiDjsAqoPKhsdF72lj8,53904
+biopipen/scripts/tcr/GIANA/GIANA4.py,sha256=zqECkRfg6lJUaOLTSnocTDrGbUWCYpjXBAwCBBHaouY,53864
 biopipen/scripts/tcr/GIANA/Imgt_Human_TRBV.fasta,sha256=XUwDPXJxVH5O9Q0gCL6EILKXEwVyiAZXm4VS2vkPcnQ,15371
 biopipen/scripts/tcr/GIANA/query.py,sha256=YJeCk24Hab7XfQxZ5VNesdjr_LVxPH0KH9rwGm1ePf4,7680
 biopipen/scripts/tcr/Immunarch-basic.R,sha256=err_gEKyx6OcxhbP2GVSaNV-mNlwHlrzxZJbUp2NiNY,3289
@@ -235,12 +234,12 @@ biopipen/scripts/tcr/ImmunarchFilter.R,sha256=-en-zi0ZB1JjuqhPlaEAN8YvHrELZNJ1V7
 biopipen/scripts/tcr/ImmunarchLoading.R,sha256=u3o2aag_7cZ17HA8RxpN58wvrII0Uh-q6FY6dA8MWeQ,5756
 biopipen/scripts/tcr/ImmunarchSplitIdents.R,sha256=FGCeGV0uSmFU91lKkldUAeV4A2m3hHw5X4GNi8ffGzI,1873
 biopipen/scripts/tcr/SampleDiversity.R,sha256=oipN4-2nQZe8bYjI0lZ0SvZ7T8GZ_FWkpkobi1cwmWE,2664
-biopipen/scripts/tcr/ScRepCombiningExpression.R,sha256=IJ7wHFKL5STWPv-mtWWt1-Ly_Evei146U0y0ZB9jCGE,933
-biopipen/scripts/tcr/ScRepLoading.R,sha256=eqJXTXn_HyLRo98Hv6xI_AmYp5l2LxHsyrMSXWZ_HmM,5167
+biopipen/scripts/tcr/ScRepCombiningExpression.R,sha256=TwnlUWG9isSl7H1VqhFLbWlVSdDwFRVSszqbnShH_E0,1011
+biopipen/scripts/tcr/ScRepLoading.R,sha256=FORXYfeTitFr9EtfJrv2A-2GeWG-WKDBBANeeT9ejds,5269
 biopipen/scripts/tcr/TCRClusterStats.R,sha256=ns3S95DVDBuhSe1YgTZ1OksbfBgREO2Tnp1d4QzbTw0,13530
-biopipen/scripts/tcr/TCRClustering.R,sha256=b-IZeE3Rcue4Ntn9H7FLljELzycbWCyKP17LlBCuMW0,9658
+biopipen/scripts/tcr/TCRClustering.R,sha256=K01qYLNhXrMmPb3TJE504lpRXnfizUNZ5q75nL7dxBg,9152
 biopipen/scripts/tcr/TCRDock.py,sha256=Oyw27k6vr0pnJ0w1-lrk5b6sZ_IOf6TmbhSxQae-3Q8,3148
-biopipen/scripts/tcr/TESSA.R,sha256=FRymeD9xYScKEMbl_OjW_sbEvQmTpXRqHaAFQaCBm1k,5756
+biopipen/scripts/tcr/TESSA.R,sha256=iXkgQMEP2OlrhdjQ0lHSdH6ehqMXBry__0KVifddWVE,5871
 biopipen/scripts/tcr/TESSA_source/Atchley_factors.csv,sha256=SumqDOqP67P54uM7Cuc5_O_rySTWcGo7eX3psMSPX9s,763
 biopipen/scripts/tcr/TESSA_source/BriseisEncoder.py,sha256=z4_Q_6StymffuUGGjHP1-B3aTsXtamKao5Q1-Kg9has,6831
 biopipen/scripts/tcr/TESSA_source/MCMC_control.R,sha256=93Nnz0IG8KfFnVscZDvmBp1qccZoSoG_jIVpOWBQLHE,2911
@@ -285,7 +284,7 @@ biopipen/utils/misc.py,sha256=pDZ-INWVNqHuXYvcjmu8KqNAigkh2lsHy0BxX44CPvc,4048
 biopipen/utils/reference.py,sha256=Oc6IlA1giLxymAuI7DO-IQLHQ7-DbsWzOQE86oTDfMU,5955
 biopipen/utils/reporter.py,sha256=VwLl6xyVDWnGY7NEXyqBlkW8expKJoNQ5iTyZSELf5c,4922
 biopipen/utils/vcf.py,sha256=MmMbAtLUcKPp02jUdk9TzuET2gWSeoWn7xgoOXFysK0,9393
-biopipen-0.34.1.dist-info/METADATA,sha256=6vO3KU_HLeykxbXJA5eCO30YyAuylO2cZr_EPwaXwfc,975
-biopipen-0.34.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-biopipen-0.34.1.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
-biopipen-0.34.1.dist-info/RECORD,,
+biopipen-0.34.3.dist-info/METADATA,sha256=Eg5cvgmjcUfF9KU_Chz0omLS8g8lSUHdG3sVujIehI8,975
+biopipen-0.34.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+biopipen-0.34.3.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
+biopipen-0.34.3.dist-info/RECORD,,

biopipen/reports/scrna/TopExpressingGenes.svelte

@@ -1,17 +0,0 @@
-{% from "utils/misc.liq" import report_jobs -%}
-{% from "utils/gsea.liq" import enrichr_report -%}
-<script>
-    import { Image, DataTable, Descr } from "$libs";
-    import { Accordion, AccordionItem, Tabs, Tab, TabContent, InlineNotification } from "$ccs";
-</script>
-
-
-{%- macro report_job(job, h=1) -%}
-    {{ job | render_job: h=h }}
-{%- endmacro -%}
-
-{%- macro head_job(job) -%}
-  <h1>{{job.in.srtobj | stem0 | escape}}</h1>
-{%- endmacro -%}
-
-{{ report_jobs(jobs, head_job, report_job) }}