R Under development (unstable) (2024-07-10 r86888 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(SCIntRuler) > > test_check("SCIntRuler") | | | 0% | |==================== | 33% | |======================================== | 67% | |============================================================| 100% | | | 0% | |==================== | 33% | |======================================== | 67% | |============================================================| 100% Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% PC_ 1 Positive: ENSG00000063177 RPL18, ENSG00000162244 RPL29, ENSG00000105193 RPS16, ENSG00000175787 ZNF169, ENSG00000173933 RBM4, ENSG00000257698 RP11-620J15.3, ENSG00000118518 RNF146, ENSG00000262202 SNORD3D, ENSG00000142784 WDTC1, ENSG00000260000 RP3-467N11.1 ENSG00000266967 AARSD1, ENSG00000167483 FAM129C, ENSG00000229474 PATL2, ENSG00000271858 XXcos-LUCA11.4, ENSG00000186166 CCDC84, ENSG00000085982 USP40, ENSG00000156515 HK1, ENSG00000273344 PAXIP1-AS1, ENSG00000135587 SMPD2, ENSG00000102974 CTCF ENSG00000101310 SEC23B, ENSG00000166145 SPINT1, ENSG00000146757 ZNF92, ENSG00000186265 BTLA, ENSG00000164077 MON1A, ENSG00000114631 PODXL2, ENSG00000146067 FAM193B, ENSG00000173064 HECTD4, ENSG00000099953 MMP11, ENSG00000197989 SNHG12 Negative: ENSG00000166387 PPFIBP2, ENSG00000123240 OPTN, ENSG00000082641 NFE2L1, ENSG00000197157 SND1, ENSG00000161980 POLR3K, ENSG00000158481 CD1C, ENSG00000030582 GRN, ENSG00000143228 NUF2, ENSG00000153774 CFDP1, ENSG00000072571 HMMR ENSG00000111206 FOXM1, ENSG00000143933 CALM2, ENSG00000215021 PHB2, ENSG00000156411 C14orf2, ENSG00000109046 WSB1, ENSG00000108826 MRPL27, ENSG00000116030 SUMO1, ENSG00000115128 SF3B14, ENSG00000172366 FAM195A, ENSG00000198546 ZNF511 ENSG00000238227 C9orf69, ENSG00000026025 VIM, ENSG00000131650 KREMEN2, ENSG00000088986 DYNLL1, ENSG00000127838 PNKD, ENSG00000197043 ANXA6, ENSG00000090554 FLT3LG, ENSG00000196642 RABL6, ENSG00000148950 IMMP1L, ENSG00000174886 NDUFA11 PC_ 2 Positive: ENSG00000158481 CD1C, ENSG00000239961 LILRA4, ENSG00000166228 PCBD1, ENSG00000161091 MFSD12, ENSG00000148719 DNAJB12, ENSG00000198715 C1orf85, ENSG00000072518 MARK2, ENSG00000107581 EIF3A, ENSG00000173559 NABP1, ENSG00000178971 CTC1 ENSG00000215021 PHB2, ENSG00000176619 LMNB2, ENSG00000127527 EPS15L1, ENSG00000100083 GGA1, ENSG00000172366 FAM195A, ENSG00000063177 RPL18, ENSG00000150776 C11orf57, ENSG00000164088 PPM1M, ENSG00000198700 IPO9, ENSG00000167522 ANKRD11 ENSG00000137404 NRM, ENSG00000095059 DHPS, ENSG00000213741 RPS29, ENSG00000196954 CASP4, ENSG00000108590 MED31, ENSG00000039650 PNKP, ENSG00000121060 TRIM25, ENSG00000020633 RUNX3, ENSG00000214367 HAUS3, ENSG00000125637 PSD4 Negative: ENSG00000090554 FLT3LG, ENSG00000126368 NR1D1, ENSG00000120915 EPHX2, ENSG00000196642 RABL6, ENSG00000159496 RGL4, ENSG00000166971 AKTIP, ENSG00000269089 AP003733.1, ENSG00000020256 ZFP64, ENSG00000229539 RP11-119B16.2, ENSG00000105829 BET1 ENSG00000160087 UBE2J2, ENSG00000155366 RHOC, ENSG00000128191 DGCR8, ENSG00000187118 CMC1, ENSG00000156411 C14orf2, ENSG00000100983 GSS, ENSG00000154473 BUB3, ENSG00000080822 CLDND1, ENSG00000198130 HIBCH, ENSG00000139197 PEX5 ENSG00000178773 CPNE7, ENSG00000150054 MPP7, ENSG00000155438 NIFK, ENSG00000273247 RP11-83A24.2, ENSG00000153774 CFDP1, ENSG00000171302 CANT1, ENSG00000197043 ANXA6, ENSG00000102409 BEX4, ENSG00000236104 ZBTB22, ENSG00000163960 UBXN7 PC_ 3 Positive: ENSG00000166387 PPFIBP2, ENSG00000170540 ARL6IP1, ENSG00000137133 HINT2, ENSG00000136527 TRA2B, ENSG00000273080 RP11-301O19.1, ENSG00000161980 POLR3K, ENSG00000196642 RABL6, ENSG00000153896 ZNF599, ENSG00000082641 NFE2L1, ENSG00000131378 RFTN1 ENSG00000121064 SCPEP1, ENSG00000186265 BTLA, ENSG00000187118 CMC1, ENSG00000128191 DGCR8, ENSG00000003249 DBNDD1, ENSG00000105193 RPS16, ENSG00000197157 SND1, ENSG00000170606 HSPA4, ENSG00000116030 SUMO1, ENSG00000153774 CFDP1 ENSG00000197989 SNHG12, ENSG00000165934 CPSF2, ENSG00000167522 ANKRD11, ENSG00000233937 CTC-338M12.4, ENSG00000128039 SRD5A3, ENSG00000225828 FAM229A, ENSG00000198026 ZNF335, ENSG00000149311 ATM, ENSG00000102409 BEX4, ENSG00000160741 CRTC2 Negative: ENSG00000126368 NR1D1, ENSG00000020256 ZFP64, ENSG00000120915 EPHX2, ENSG00000170175 CHRNB1, ENSG00000269089 AP003733.1, ENSG00000171302 CANT1, ENSG00000110330 BIRC2, ENSG00000198546 ZNF511, ENSG00000150054 MPP7, ENSG00000178773 CPNE7 ENSG00000139197 PEX5, ENSG00000090554 FLT3LG, ENSG00000148950 IMMP1L, ENSG00000168303 MPLKIP, ENSG00000167543 TP53I13, ENSG00000229539 RP11-119B16.2, ENSG00000005001 PRSS22, ENSG00000273247 RP11-83A24.2, ENSG00000114503 NCBP2, ENSG00000120948 TARDBP ENSG00000239961 LILRA4, ENSG00000054148 PHPT1, ENSG00000090447 TFAP4, ENSG00000161091 MFSD12, ENSG00000257704 PRR24, ENSG00000148719 DNAJB12, ENSG00000173559 NABP1, ENSG00000160087 UBE2J2, ENSG00000243279 PRAF2, ENSG00000125637 PSD4 PC_ 4 Positive: ENSG00000159496 RGL4, ENSG00000187118 CMC1, ENSG00000273080 RP11-301O19.1, ENSG00000090554 FLT3LG, ENSG00000163960 UBXN7, ENSG00000143933 CALM2, ENSG00000105619 TFPT, ENSG00000131378 RFTN1, ENSG00000167118 URM1, ENSG00000020633 RUNX3 ENSG00000181396 OGFOD3, ENSG00000089123 TASP1, ENSG00000196954 CASP4, ENSG00000162076 FLYWCH2, ENSG00000198715 C1orf85, ENSG00000236104 ZBTB22, ENSG00000121064 SCPEP1, ENSG00000125743 SNRPD2, ENSG00000162620 LRRIQ3, ENSG00000136819 C9orf78 ENSG00000136717 BIN1, ENSG00000100983 GSS, ENSG00000145414 NAF1, ENSG00000166971 AKTIP, ENSG00000137133 HINT2, ENSG00000142856 ITGB3BP, ENSG00000150776 C11orf57, ENSG00000115806 GORASP2, ENSG00000108591 DRG2, ENSG00000116030 SUMO1 Negative: ENSG00000047932 GOPC, ENSG00000166387 PPFIBP2, ENSG00000143228 NUF2, ENSG00000082641 NFE2L1, ENSG00000080822 CLDND1, ENSG00000160741 CRTC2, ENSG00000172366 FAM195A, ENSG00000111224 PARP11, ENSG00000095059 DHPS, ENSG00000143353 LYPLAL1 ENSG00000260000 RP3-467N11.1, ENSG00000238227 C9orf69, ENSG00000168303 MPLKIP, ENSG00000247240 UBL7-AS1, ENSG00000072571 HMMR, ENSG00000111206 FOXM1, ENSG00000271858 XXcos-LUCA11.4, ENSG00000197043 ANXA6, ENSG00000273344 PAXIP1-AS1, ENSG00000148840 PPRC1 ENSG00000099953 MMP11, ENSG00000173064 HECTD4, ENSG00000128039 SRD5A3, ENSG00000257698 RP11-620J15.3, ENSG00000165934 CPSF2, ENSG00000165733 BMS1, ENSG00000171302 CANT1, ENSG00000105058 FAM32A, ENSG00000198026 ZNF335, ENSG00000100348 TXN2 PC_ 5 Positive: ENSG00000126756 UXT, ENSG00000116221 MRPL37, ENSG00000164327 RICTOR, ENSG00000100564 PIGH, ENSG00000167483 FAM129C, ENSG00000165733 BMS1, ENSG00000128039 SRD5A3, ENSG00000143353 LYPLAL1, ENSG00000181396 OGFOD3, ENSG00000105193 RPS16 ENSG00000109919 MTCH2, ENSG00000163162 RNF149, ENSG00000080822 CLDND1, ENSG00000111666 CHPT1, ENSG00000030582 GRN, ENSG00000143228 NUF2, ENSG00000160688 FLAD1, ENSG00000148840 PPRC1, ENSG00000150776 C11orf57, ENSG00000108826 MRPL27 ENSG00000113593 PPWD1, ENSG00000247240 UBL7-AS1, ENSG00000184752 NDUFA12, ENSG00000196262 PPIA, ENSG00000092036 HAUS4, ENSG00000197157 SND1, ENSG00000146828 SLC12A9, ENSG00000148719 DNAJB12, ENSG00000161980 POLR3K, ENSG00000174886 NDUFA11 Negative: ENSG00000137404 NRM, ENSG00000100083 GGA1, ENSG00000260000 RP3-467N11.1, ENSG00000118518 RNF146, ENSG00000172366 FAM195A, ENSG00000198026 ZNF335, ENSG00000173064 HECTD4, ENSG00000173933 RBM4, ENSG00000162620 LRRIQ3, ENSG00000128191 DGCR8 ENSG00000273344 PAXIP1-AS1, ENSG00000158481 CD1C, ENSG00000153896 ZNF599, ENSG00000164077 MON1A, ENSG00000125743 SNRPD2, ENSG00000268472 AP002884.2, ENSG00000099953 MMP11, ENSG00000271858 XXcos-LUCA11.4, ENSG00000089123 TASP1, ENSG00000162928 PEX13 ENSG00000198715 C1orf85, ENSG00000198130 HIBCH, ENSG00000166971 AKTIP, ENSG00000170606 HSPA4, ENSG00000233937 CTC-338M12.4, ENSG00000156411 C14orf2, ENSG00000186265 BTLA, ENSG00000241837 ATP5O, ENSG00000135916 ITM2C, ENSG00000175787 ZNF169 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 336 Number of edges: 22882 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5000 Number of communities: 1 Elapsed time: 0 seconds Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% PC_ 1 Positive: ENSG00000144746 ARL6IP5, ENSG00000198821 CD247, ENSG00000256060 TRAPPC2P1, ENSG00000260083 MIR4519, ENSG00000027075 PRKCH, ENSG00000143570 SLC39A1, ENSG00000174059 CD34, ENSG00000177398 UMODL1, ENSG00000175893 ZDHHC21, ENSG00000167483 FAM129C ENSG00000048991 R3HDM1, ENSG00000263508 RP11-963H4.3, ENSG00000235106 LINC00094, ENSG00000132382 MYBBP1A, ENSG00000155252 PI4K2A, ENSG00000126749 EMG1, ENSG00000153107 ANAPC1, ENSG00000184154 LRTOMT, ENSG00000204564 C6orf136, ENSG00000099992 TBC1D10A ENSG00000105193 RPS16, ENSG00000109787 KLF3, ENSG00000143167 GPA33, ENSG00000186265 BTLA, ENSG00000180096 SEPT1, ENSG00000189339 SLC35E2B, ENSG00000237438 CECR7, ENSG00000271858 XXcos-LUCA11.4, ENSG00000121897 LIAS, ENSG00000138138 ATAD1 Negative: ENSG00000119411 BSPRY, ENSG00000085788 DDHD2, ENSG00000156170 NDUFAF6, ENSG00000197780 TAF13, ENSG00000164305 CASP3, ENSG00000171848 RRM2, ENSG00000182359 KBTBD3, ENSG00000075234 TTC38, ENSG00000184451 CCR10, ENSG00000213676 ATF6B ENSG00000167522 ANKRD11, ENSG00000136152 COG3, ENSG00000055163 CYFIP2, ENSG00000173064 HECTD4, ENSG00000137074 APTX, ENSG00000159884 CCDC107, ENSG00000099956 SMARCB1, ENSG00000104774 MAN2B1, ENSG00000223865 HLA-DPB1, ENSG00000104047 DTWD1 ENSG00000198546 ZNF511, ENSG00000100124 ANKRD54, ENSG00000129534 MIS18BP1, ENSG00000241370 RPP21, ENSG00000215021 PHB2, ENSG00000254470 AP5B1, ENSG00000198951 NAGA, ENSG00000025708 TYMP, ENSG00000100416 TRMU, ENSG00000272269 RP11-500C11.3 PC_ 2 Positive: ENSG00000223865 HLA-DPB1, ENSG00000025708 TYMP, ENSG00000124570 SERPINB6, ENSG00000204482 LST1, ENSG00000173064 HECTD4, ENSG00000198951 NAGA, ENSG00000130475 FCHO1, ENSG00000124357 NAGK, ENSG00000100908 EMC9, ENSG00000197223 C1D ENSG00000161243 FBXO27, ENSG00000198498 TMA16, ENSG00000163251 FZD5, ENSG00000168303 MPLKIP, ENSG00000160326 SLC2A6, ENSG00000229117 RPL41, ENSG00000139719 VPS33A, ENSG00000174652 ZNF266, ENSG00000090621 PABPC4, ENSG00000084234 APLP2 ENSG00000100416 TRMU, ENSG00000163040 CCDC74A, ENSG00000167536 DHRS13, ENSG00000272269 RP11-500C11.3, ENSG00000166333 ILK, ENSG00000273080 RP11-301O19.1, ENSG00000087076 HSD17B14, ENSG00000238227 C9orf69, ENSG00000247240 UBL7-AS1, ENSG00000121644 DESI2 Negative: ENSG00000119411 BSPRY, ENSG00000171848 RRM2, ENSG00000197780 TAF13, ENSG00000164305 CASP3, ENSG00000085788 DDHD2, ENSG00000156170 NDUFAF6, ENSG00000180096 SEPT1, ENSG00000184451 CCR10, ENSG00000243279 PRAF2, ENSG00000100124 ANKRD54 ENSG00000075234 TTC38, ENSG00000055163 CYFIP2, ENSG00000198821 CD247, ENSG00000271858 XXcos-LUCA11.4, ENSG00000143353 LYPLAL1, ENSG00000104047 DTWD1, ENSG00000080822 CLDND1, ENSG00000144746 ARL6IP5, ENSG00000126756 UXT, ENSG00000256060 TRAPPC2P1 ENSG00000027075 PRKCH, ENSG00000136152 COG3, ENSG00000048991 R3HDM1, ENSG00000263508 RP11-963H4.3, ENSG00000167483 FAM129C, ENSG00000174059 CD34, ENSG00000177398 UMODL1, ENSG00000175893 ZDHHC21, ENSG00000079246 XRCC5, ENSG00000241370 RPP21 PC_ 3 Positive: ENSG00000138138 ATAD1, ENSG00000177398 UMODL1, ENSG00000174059 CD34, ENSG00000263508 RP11-963H4.3, ENSG00000175893 ZDHHC21, ENSG00000167483 FAM129C, ENSG00000048991 R3HDM1, ENSG00000256060 TRAPPC2P1, ENSG00000143570 SLC39A1, ENSG00000155252 PI4K2A ENSG00000271858 XXcos-LUCA11.4, ENSG00000135916 ITM2C, ENSG00000109787 KLF3, ENSG00000099991 CABIN1, ENSG00000249222 ATP5L2, ENSG00000136527 TRA2B, ENSG00000118705 RPN2, ENSG00000185650 ZFP36L1, ENSG00000197223 C1D, ENSG00000161243 FBXO27 ENSG00000238227 C9orf69, ENSG00000247240 UBL7-AS1, ENSG00000087076 HSD17B14, ENSG00000116030 SUMO1, ENSG00000170540 ARL6IP1, ENSG00000100908 EMC9, ENSG00000243279 PRAF2, ENSG00000153130 SCOC, ENSG00000168090 COPS6, ENSG00000118680 MYL12B Negative: ENSG00000127774 EMC6, ENSG00000025708 TYMP, ENSG00000229117 RPL41, ENSG00000105193 RPS16, ENSG00000126749 EMG1, ENSG00000173221 GLRX, ENSG00000136867 SLC31A2, ENSG00000205246 RPSAP58, ENSG00000184752 NDUFA12, ENSG00000137193 PIM1 ENSG00000027075 PRKCH, ENSG00000170606 HSPA4, ENSG00000164733 CTSB, ENSG00000257704 PRR24, ENSG00000180509 KCNE1, ENSG00000184451 CCR10, ENSG00000075234 TTC38, ENSG00000139233 LLPH, ENSG00000172366 FAM195A, ENSG00000205758 CRYZL1 ENSG00000143353 LYPLAL1, ENSG00000104774 MAN2B1, ENSG00000137474 MYO7A, ENSG00000163162 RNF149, ENSG00000115828 QPCT, ENSG00000184277 TM2D3, ENSG00000160888 IER2, ENSG00000091009 RBM27, ENSG00000132382 MYBBP1A, ENSG00000105341 ATP5SL PC_ 4 Positive: ENSG00000204482 LST1, ENSG00000025708 TYMP, ENSG00000223865 HLA-DPB1, ENSG00000136867 SLC31A2, ENSG00000229117 RPL41, ENSG00000155252 PI4K2A, ENSG00000164733 CTSB, ENSG00000263508 RP11-963H4.3, ENSG00000175893 ZDHHC21, ENSG00000177398 UMODL1 ENSG00000167483 FAM129C, ENSG00000048991 R3HDM1, ENSG00000174059 CD34, ENSG00000124357 NAGK, ENSG00000065989 PDE4A, ENSG00000249222 ATP5L2, ENSG00000180509 KCNE1, ENSG00000170606 HSPA4, ENSG00000143570 SLC39A1, ENSG00000127774 EMC6 ENSG00000136152 COG3, ENSG00000184277 TM2D3, ENSG00000127616 SMARCA4, ENSG00000075234 TTC38, ENSG00000115828 QPCT, ENSG00000254470 AP5B1, ENSG00000104774 MAN2B1, ENSG00000091106 NLRC4, ENSG00000138646 HERC5, ENSG00000084234 APLP2 Negative: ENSG00000136717 BIN1, ENSG00000170248 PDCD6IP, ENSG00000074755 ZZEF1, ENSG00000164088 PPM1M, ENSG00000162244 RPL29, ENSG00000126756 UXT, ENSG00000198821 CD247, ENSG00000174652 ZNF266, ENSG00000260796 RP11-1348G14.5, ENSG00000105829 BET1 ENSG00000118705 RPN2, ENSG00000143575 HAX1, ENSG00000172717 FAM71D, ENSG00000183431 SF3A3, ENSG00000134882 UBAC2, ENSG00000142892 PIGK, ENSG00000107771 CCSER2, ENSG00000180096 SEPT1, ENSG00000132424 PNISR, ENSG00000173064 HECTD4 ENSG00000155330 C16orf87, ENSG00000197157 SND1, ENSG00000205758 CRYZL1, ENSG00000161243 FBXO27, ENSG00000080822 CLDND1, ENSG00000198498 TMA16, ENSG00000153130 SCOC, ENSG00000132382 MYBBP1A, ENSG00000105329 TGFB1, ENSG00000099992 TBC1D10A PC_ 5 Positive: ENSG00000197223 C1D, ENSG00000139719 VPS33A, ENSG00000100908 EMC9, ENSG00000168303 MPLKIP, ENSG00000183431 SF3A3, ENSG00000115128 SF3B14, ENSG00000161243 FBXO27, ENSG00000163251 FZD5, ENSG00000143575 HAX1, ENSG00000197912 SPG7 ENSG00000145545 SRD5A1, ENSG00000087076 HSD17B14, ENSG00000238227 C9orf69, ENSG00000247240 UBL7-AS1, ENSG00000273080 RP11-301O19.1, ENSG00000102967 DHODH, ENSG00000153130 SCOC, ENSG00000141452 C18orf8, ENSG00000104885 DOT1L, ENSG00000169710 FASN ENSG00000130475 FCHO1, ENSG00000213676 ATF6B, ENSG00000241990 RP6-109B7.3, ENSG00000090621 PABPC4, ENSG00000249222 ATP5L2, ENSG00000120699 EXOSC8, ENSG00000116030 SUMO1, ENSG00000160326 SLC2A6, ENSG00000173064 HECTD4, ENSG00000137133 HINT2 Negative: ENSG00000074755 ZZEF1, ENSG00000063761 ADCK1, ENSG00000257303 RP11-977G19.11, ENSG00000096968 JAK2, ENSG00000197471 SPN, ENSG00000121644 DESI2, ENSG00000107771 CCSER2, ENSG00000143207 RFWD2, ENSG00000198951 NAGA, ENSG00000105829 BET1 ENSG00000260796 RP11-1348G14.5, ENSG00000107581 EIF3A, ENSG00000109534 GAR1, ENSG00000167766 ZNF83, ENSG00000099991 CABIN1, ENSG00000129158 SERGEF, ENSG00000073803 MAP3K13, ENSG00000172717 FAM71D, ENSG00000167543 TP53I13, ENSG00000204482 LST1 ENSG00000159884 CCDC107, ENSG00000105341 ATP5SL, ENSG00000083844 ZNF264, ENSG00000170248 PDCD6IP, ENSG00000164088 PPM1M, ENSG00000129534 MIS18BP1, ENSG00000025708 TYMP, ENSG00000134882 UBAC2, ENSG00000223865 HLA-DPB1, ENSG00000124357 NAGK Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 136 Number of edges: 6749 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5543 Number of communities: 2 Elapsed time: 0 seconds Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% PC_ 1 Positive: ENSG00000101474 APMAP, ENSG00000213741 RPS29, ENSG00000158805 ZNF276, ENSG00000184007 PTP4A2, ENSG00000186010 NDUFA13, ENSG00000130770 ATPIF1, ENSG00000124570 SERPINB6, ENSG00000099330 OCEL1, ENSG00000139725 RHOF, ENSG00000130703 OSBPL2 ENSG00000168701 TMEM208, ENSG00000118680 MYL12B, ENSG00000125995 ROMO1, ENSG00000241370 RPP21, ENSG00000178691 SUZ12, ENSG00000120699 EXOSC8, ENSG00000102309 PIN4, ENSG00000116237 ICMT, ENSG00000113391 FAM172A, ENSG00000020633 RUNX3 ENSG00000164305 CASP3, ENSG00000164031 DNAJB14, ENSG00000007080 CCDC124, ENSG00000141002 TCF25, ENSG00000123240 OPTN, ENSG00000115128 SF3B14, ENSG00000153107 ANAPC1, ENSG00000075089 ACTR6, ENSG00000170540 ARL6IP1, ENSG00000143553 SNAPIN Negative: ENSG00000139193 CD27, ENSG00000026025 VIM, ENSG00000162244 RPL29, ENSG00000090554 FLT3LG, ENSG00000063177 RPL18, ENSG00000095059 DHPS, ENSG00000100129 EIF3L, ENSG00000197880 MDS2, ENSG00000134202 GSTM3, ENSG00000173327 MAP3K11 ENSG00000204482 LST1, ENSG00000198355 PIM3, ENSG00000205246 RPSAP58, ENSG00000168101 NUDT16L1, ENSG00000179598 PLD6, ENSG00000180376 CCDC66, ENSG00000169100 SLC25A6, ENSG00000131368 MRPS25, ENSG00000266947 RP11-799D4.4, ENSG00000167536 DHRS13 ENSG00000254802 AC022182.3, ENSG00000253276 CCDC71L, ENSG00000168209 DDIT4, ENSG00000163162 RNF149, ENSG00000196505 GDAP2, ENSG00000128944 KNSTRN, ENSG00000144524 COPS7B, ENSG00000146828 SLC12A9, ENSG00000111877 MCM9, ENSG00000160685 ZBTB7B PC_ 2 Positive: ENSG00000153107 ANAPC1, ENSG00000113391 FAM172A, ENSG00000197841 ZNF181, ENSG00000169499 PLEKHA2, ENSG00000100359 SGSM3, ENSG00000273117 AC144652.1, ENSG00000136811 ODF2, ENSG00000064651 SLC12A2, ENSG00000223759 RP11-353N4.4, ENSG00000135365 PHF21A ENSG00000211456 SACM1L, ENSG00000106524 ANKMY2, ENSG00000240291 RP11-499P20.2, ENSG00000153140 CETN3, ENSG00000105993 DNAJB6, ENSG00000241839 PLEKHO2, ENSG00000115128 SF3B14, ENSG00000259230 CTD-2555C10.3, ENSG00000125995 ROMO1, ENSG00000100983 GSS ENSG00000130770 ATPIF1, ENSG00000184277 TM2D3, ENSG00000142892 PIGK, ENSG00000075089 ACTR6, ENSG00000168958 MFF, ENSG00000125482 TTF1, ENSG00000106245 BUD31, ENSG00000164305 CASP3, ENSG00000197043 ANXA6, ENSG00000139668 WDFY2 Negative: ENSG00000130703 OSBPL2, ENSG00000206053 HN1L, ENSG00000186376 ZNF75D, ENSG00000102309 PIN4, ENSG00000164031 DNAJB14, ENSG00000060339 CCAR1, ENSG00000030582 GRN, ENSG00000170248 PDCD6IP, ENSG00000084072 PPIE, ENSG00000115520 COQ10B ENSG00000116237 ICMT, ENSG00000120742 SERP1, ENSG00000143353 LYPLAL1, ENSG00000166228 PCBD1, ENSG00000099991 CABIN1, ENSG00000054148 PHPT1, ENSG00000146828 SLC12A9, ENSG00000082805 ERC1, ENSG00000164088 PPM1M, ENSG00000105866 SP4 ENSG00000181847 TIGIT, ENSG00000175756 AURKAIP1, ENSG00000171204 TMEM126B, ENSG00000155592 ZKSCAN2, ENSG00000106603 COA1, ENSG00000167522 ANKRD11, ENSG00000165675 ENOX2, ENSG00000004468 CD38, ENSG00000166224 SGPL1, ENSG00000120697 ALG5 PC_ 3 Positive: ENSG00000170540 ARL6IP1, ENSG00000101052 IFT52, ENSG00000116497 S100PBP, ENSG00000150347 ARID5B, ENSG00000082701 GSK3B, ENSG00000149823 VPS51, ENSG00000137411 VARS2, ENSG00000168090 COPS6, ENSG00000102309 PIN4, ENSG00000164733 CTSB ENSG00000131368 MRPS25, ENSG00000153814 JAZF1, ENSG00000126457 PRMT1, ENSG00000270170 NCBP2-AS2, ENSG00000187514 PTMA, ENSG00000134014 ELP3, ENSG00000237441 RGL2, ENSG00000123240 OPTN, ENSG00000116906 GNPAT, ENSG00000100983 GSS ENSG00000187257 RSBN1L, ENSG00000169032 MAP2K1, ENSG00000141452 C18orf8, ENSG00000060339 CCAR1, ENSG00000105329 TGFB1, ENSG00000214106 PAXIP1-AS2, ENSG00000129317 PUS7L, ENSG00000213741 RPS29, ENSG00000228857 AC104653.1, ENSG00000173457 PPP1R14B Negative: ENSG00000026025 VIM, ENSG00000113391 FAM172A, ENSG00000116237 ICMT, ENSG00000120699 EXOSC8, ENSG00000130703 OSBPL2, ENSG00000137601 NEK1, ENSG00000150776 C11orf57, ENSG00000153107 ANAPC1, ENSG00000063177 RPL18, ENSG00000169100 SLC25A6 ENSG00000197841 ZNF181, ENSG00000206053 HN1L, ENSG00000082805 ERC1, ENSG00000168209 DDIT4, ENSG00000106603 COA1, ENSG00000100348 TXN2, ENSG00000156170 NDUFAF6, ENSG00000100359 SGSM3, ENSG00000273117 AC144652.1, ENSG00000162496 DHRS3 ENSG00000171204 TMEM126B, ENSG00000184277 TM2D3, ENSG00000106524 ANKMY2, ENSG00000161526 SAP30BP, ENSG00000117335 CD46, ENSG00000100129 EIF3L, ENSG00000120742 SERP1, ENSG00000135587 SMPD2, ENSG00000105866 SP4, ENSG00000064651 SLC12A2 PC_ 4 Positive: ENSG00000174456 C12orf76, ENSG00000168101 NUDT16L1, ENSG00000139668 WDFY2, ENSG00000013288 MAN2B2, ENSG00000120699 EXOSC8, ENSG00000085788 DDHD2, ENSG00000099849 RASSF7, ENSG00000160685 ZBTB7B, ENSG00000120697 ALG5, ENSG00000106245 BUD31 ENSG00000241839 PLEKHO2, ENSG00000164305 CASP3, ENSG00000228857 AC104653.1, ENSG00000158805 ZNF276, ENSG00000164031 DNAJB14, ENSG00000148218 ALAD, ENSG00000197223 C1D, ENSG00000111666 CHPT1, ENSG00000082701 GSK3B, ENSG00000257303 RP11-977G19.11 ENSG00000101474 APMAP, ENSG00000213741 RPS29, ENSG00000060339 CCAR1, ENSG00000129317 PUS7L, ENSG00000150776 C11orf57, ENSG00000125482 TTF1, ENSG00000142892 PIGK, ENSG00000102309 PIN4, ENSG00000189227 C15orf61, ENSG00000104518 GSDMD Negative: ENSG00000113391 FAM172A, ENSG00000173933 RBM4, ENSG00000154930 ACSS1, ENSG00000241370 RPP21, ENSG00000099991 CABIN1, ENSG00000196591 HDAC2, ENSG00000109787 KLF3, ENSG00000161204 ABCF3, ENSG00000138138 ATAD1, ENSG00000240291 RP11-499P20.2 ENSG00000168958 MFF, ENSG00000257704 PRR24, ENSG00000168090 COPS6, ENSG00000143553 SNAPIN, ENSG00000072518 MARK2, ENSG00000142856 ITGB3BP, ENSG00000135365 PHF21A, ENSG00000197841 ZNF181, ENSG00000260077 RP11-254F7.2, ENSG00000166133 RPUSD2 ENSG00000146828 SLC12A9, ENSG00000143353 LYPLAL1, ENSG00000132549 VPS13B, ENSG00000273117 AC144652.1, ENSG00000106524 ANKMY2, ENSG00000182359 KBTBD3, ENSG00000172500 FIBP, ENSG00000174100 MRPL45, ENSG00000254802 AC022182.3, ENSG00000134516 DOCK2 PC_ 5 Positive: ENSG00000082701 GSK3B, ENSG00000113391 FAM172A, ENSG00000164305 CASP3, ENSG00000163162 RNF149, ENSG00000116497 S100PBP, ENSG00000109787 KLF3, ENSG00000186376 ZNF75D, ENSG00000237441 RGL2, ENSG00000173327 MAP3K11, ENSG00000060339 CCAR1 ENSG00000141452 C18orf8, ENSG00000120742 SERP1, ENSG00000161526 SAP30BP, ENSG00000270170 NCBP2-AS2, ENSG00000197841 ZNF181, ENSG00000143553 SNAPIN, ENSG00000102309 PIN4, ENSG00000159479 MED8, ENSG00000170540 ARL6IP1, ENSG00000144524 COPS7B ENSG00000099849 RASSF7, ENSG00000164366 CCDC127, ENSG00000166224 SGPL1, ENSG00000136811 ODF2, ENSG00000228857 AC104653.1, ENSG00000214106 PAXIP1-AS2, ENSG00000106524 ANKMY2, ENSG00000109920 FNBP4, ENSG00000226742 HSBP1L1, ENSG00000260464 RP4-561L24.3 Negative: ENSG00000148248 SURF4, ENSG00000105341 ATP5SL, ENSG00000106367 AP1S1, ENSG00000092201 SUPT16H, ENSG00000123240 OPTN, ENSG00000272606 RP11-554J4.1, ENSG00000146729 GBAS, ENSG00000118518 RNF146, ENSG00000136169 SETDB2, ENSG00000166979 EVA1C ENSG00000130770 ATPIF1, ENSG00000173442 EHBP1L1, ENSG00000111666 CHPT1, ENSG00000169905 TOR1AIP2, ENSG00000126457 PRMT1, ENSG00000272831 RP11-792A8.4, ENSG00000164970 FAM219A, ENSG00000090621 PABPC4, ENSG00000079246 XRCC5, ENSG00000160685 ZBTB7B ENSG00000106683 LIMK1, ENSG00000169032 MAP2K1, ENSG00000020633 RUNX3, ENSG00000085788 DDHD2, ENSG00000196642 RABL6, ENSG00000108349 CASC3, ENSG00000137601 NEK1, ENSG00000105993 DNAJB6, ENSG00000074755 ZZEF1, ENSG00000164088 PPM1M Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 328 Number of edges: 24584 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5000 Number of communities: 1 Elapsed time: 0 seconds [ FAIL 0 | WARN 28 | SKIP 0 | PASS 8 ] [ FAIL 0 | WARN 28 | SKIP 0 | PASS 8 ] > > proc.time() user system elapsed 24.92 2.59 27.67