Get broad and fine clusters
GetCluster(seuratlist, n1 = 50, n2 = 200)A list of Seurat objects, usually can be got by SplitObject(). We also accept the SingleCellExperiment object input.
If the number of cells was smaller than n1, then the cluster will remain unchanged called rare cluster. The default value of n1 is 50.
If the count of cells within a broad cluster is more than n2, the cluster is subdivided randomly into three fine clusters. If the cell count falls within the range of n1 to n2, two fine clusters are generated randomly. Default value is 200.
A list of data frames.
data(sim_data_sce)
# Assuming "seuratlist" is a list of Seurat objects
# if(is(sim_data_sce, "SingleCellExperiment")){ sim_data <- as.Seurat(sim_data_sce) }
sim_data <- SCEtoSeurat(sim_data_sce)
#> Warning: No gene metadata columns found to add to Seurat object.
seuratlist <- Seurat::SplitObject(sim_data, split.by = "Study")
# seuratlist <- InputData(sim_data_sce,"Study")
fullcluster <- GetCluster(seuratlist)
#> Normalizing layer: counts
#> Finding variable features for layer counts
#> Warning: pseudoinverse used at -2.5443
#> Warning: neighborhood radius 0.31902
#> Warning: reciprocal condition number 0
#> Warning: There are other near singularities as well. 0.090619
#> Centering and scaling data matrix
#> Warning: The following 994 features requested have zero variance; running reduction without them: ENSG00000172733 PURG, ENSG00000180209 MYLPF, ENSG00000261231 RP11-523L20.2, ENSG00000189367 KIAA0408, ENSG00000086570 FAT2, ENSG00000249882 RP11-665I14.1, ENSG00000237853 RP5-833A20.1, ENSG00000255276 RRM1-AS1, ENSG00000224902 GAGE12H, ENSG00000164185 ZNF474, ENSG00000248703 RP11-495K9.3, ENSG00000251151 HOXC-AS3, ENSG00000177076 ACER2, ENSG00000267038 RP11-1096D5.2, ENSG00000228569 AC073133.2, ENSG00000260780 RP11-580I1.1, ENSG00000231703 RP4-669H2.1, ENSG00000224658 RP11-631F7.1, ENSG00000250431 RP13-577H12.2, ENSG00000231731 AC010976.2, ENSG00000255420 RP11-236J17.3, ENSG00000204889 KRT40, ENSG00000237907 RP5-1013A22.2, ENSG00000185792 NLRP9, ENSG00000272579 RP11-101E13.5, ENSG00000272121 RP4-555D20.4, ENSG00000196754 S100A2, ENSG00000251532 CTD-2245E15.3, ENSG00000125954 CHURC1-FNTB, ENSG00000168621 GDNF, ENSG00000224844 AC107079.1, ENSG00000139988 RDH12, ENSG00000132693 CRP, ENSG00000174032 SLC25A30, ENSG00000257985 RP1-228P16.4, ENSG00000261583 CTD-2385L22.1, ENSG00000172260 NEGR1, ENSG00000230687 RP5-1114G22.2, ENSG00000261789 RP11-709D24.5, ENSG00000065320 NTN1, ENSG00000267467 APOC4, ENSG00000006788 MYH13, ENSG00000234622 RP13-297E16.5, ENSG00000233234 RP11-740P5.2, ENSG00000269064 AL160286.1, ENSG00000269895 AP000654.4, ENSG00000267580 CTD-2540B15.11, ENSG00000265778 RP11-17M16.2, ENSG00000269199 AC003973.5, ENSG00000184492 FOXD4L1, ENSG00000249847 RP11-192C21.2, ENSG00000226113 RP11-672F9.1, ENSG00000255104 ZNF286A, ENSG00000263508 RP11-963H4.3, ENSG00000231294 AC006994.2, ENSG00000064309 CDON, ENSG00000254290 RP11-150O12.3, ENSG00000261717 RP11-77K12.1, ENSG00000184454 NCMAP, ENSG00000228539 RP11-526K17.2, ENSG00000236306 RP11-33G16.1, ENSG00000099364 FBXL19, ENSG00000204187 LINC00619, ENSG00000120436 GPR31, ENSG00000227131 RP11-552E20.1, ENSG00000245385 RP11-334E6.10, ENSG00000133131 MORC4, ENSG00000242767 ZBTB20-AS4, ENSG00000226386 PARD3-AS1, ENSG00000165309 ARMC3, ENSG00000170835 CEL, ENSG00000256391 SDIM1, ENSG00000232530 RP1-102K2.6, ENSG00000235910 APOA1-AS, ENSG00000185894 BPY2C, ENSG00000198400 NTRK1, ENSG00000258888 RP11-326A13.1, ENSG00000235085 AC091153.4, ENSG00000204702 OR2J1, ENSG00000165996 PTPLA, ENSG00000163251 FZD5, ENSG00000259818 RP5-1024G6.7, ENSG00000203301 AL590822.1, ENSG00000178412 RP11-567M16.3, ENSG00000233835 RP1-92C4.2, ENSG00000268012 AC016559.1, ENSG00000268549 RP11-295P9.8, ENSG00000175121 WFDC5, ENSG00000259063 DUX4L5, ENSG00000228213 NLGN1-AS1, ENSG00000233821 ENOX1-AS1, ENSG00000221938 OR2A14, ENSG00000091128 LAMB4, ENSG00000224691 GS1-174L6.4, ENSG00000183032 SLC25A21, ENSG00000259312 RP11-522B15.5, ENSG00000270755 RP11-138E2.1, ENSG00000145198 VWA5B2, ENSG00000174111 SOCS7, ENSG00000100012 SEC14L3, ENSG00000181074 OR52N4, ENSG00000250241 RP11-9G1.3, ENSG00000236761 CTAGE9, ENSG00000248828 RP11-673E1.4, ENSG00000204110 RP1-153P14.8, ENSG00000227518 MIR1302-9, ENSG00000224201 PNMA6A, ENSG00000225216 AC007362.3, ENSG00000251258 RFPL4B, ENSG00000249639 CTB-138E5.1, ENSG00000156486 KCNS2, ENSG00000228272 AC106874.1, ENSG00000163914 RHO, ENSG00000196532 HIST1H3C, ENSG00000256802 RP11-680F8.1, ENSG00000134853 PDGFRA, ENSG00000117479 SLC19A2, ENSG00000228214 LINC00693, ENSG00000205537 RP11-89H19.1, ENSG00000272663 RP11-191L17.1, ENSG00000229855 CTC-546K23.1, ENSG00000236463 LINC00427, ENSG00000259044 RP11-789A21.1, ENSG00000268091 AC078925.1, ENSG00000254768 CTD-2140G10.2, ENSG00000125257 ABCC4, ENSG00000268126 AC091948.1, ENSG00000272762 RP11-155D18.14, ENSG00000164236 ANKRD33B, ENSG00000123243 ITIH5, ENSG00000165066 NKX6-3, ENSG00000172382 PRSS27, ENSG00000232529 RP1-257I9.2, ENSG00000231734 RP6-206I17.2, ENSG00000222030 AC007131.1, ENSG00000203364 RP11-370F5.4, ENSG00000240553 RP1-184J9.2, ENSG00000099812 MISP, ENSG00000253893 FAM85B, ENSG00000176742 OR51V1, ENSG00000233244 CYP4F59P, ENSG00000259518 RP11-597K23.2, ENSG00000069764 PLA2G10, ENSG00000253735 RP11-115J16.3, ENSG00000230920 RP11-527D15.1, ENSG00000262576 PCDHGA4, ENSG00000130433 CACNG6, ENSG00000140993 TIGD7, ENSG00000004776 HSPB6, ENSG00000205693 MANSC4, ENSG00000273091 AP000255.6, ENSG00000143797 MBOAT2, ENSG00000170549 IRX1, ENSG00000261272 MUC22, ENSG00000227782 AC002553.1, ENSG00000115602 IL1RL1, ENSG00000176754 LINC00303, ENSG00000131480 AOC2, ENSG00000140798 ABCC12, ENSG00000164855 TMEM184A, ENSG00000233670 PIRT, ENSG00000007171 NOS2, ENSG00000226957 RP4-533D7.4, ENSG00000187730 GABRD, ENSG00000259375 RP11-815J21.2, ENSG00000255327 RP11-555G19.1, ENSG00000099377 HSD3B7, ENSG00000267769 CTB-50L17.9, ENSG00000157557 ETS2, ENSG00000227047 AC012065.4, ENSG00000206043 C18orf63, ENSG00000165985 C1QL3, ENSG00000231394 RP11-310H4.3, ENSG00000124334 IL9R, ENSG00000226209 AL138764.1, ENSG00000267191 RP11-15A1.2, ENSG00000198812 LRRC10, ENSG00000255313 RP11-1082L8.2, ENSG00000268809 AC012360.2, ENSG00000231426 RP5-899B16.1, ENSG00000224616 RP11-305E17.6, ENSG00000259714 LINC00594, ENSG00000254084 KB-1930G5.4, ENSG00000246331 RP11-77I22.2, ENSG00000130701 RBBP8NL, ENSG00000269676 MUC8, ENSG00000268923 AL645922.1, ENSG00000139797 RNF113B, ENSG00000171540 OTP, ENSG00000257918 RP11-482D24.3, ENSG00000256209 RP11-897M7.1, ENSG00000257894 RP1-78O14.1, ENSG00000182578 CSF1R, ENSG00000264750 RP11-277J6.2, ENSG00000197471 SPN, ENSG00000130822 PNCK, ENSG00000058085 LAMC2, ENSG00000243224 RP5-1157M23.2, ENSG00000167858 TEKT1, ENSG00000124813 RUNX2, ENSG00000260235 CTD-2026K11.3, ENSG00000271973 RP11-572O6.1, ENSG00000232080 XXbac-BPG254F23.7, ENSG00000231171 LINC01098, ENSG00000226310 RP3-323P24.3, ENSG00000225872 AC002398.5, ENSG00000260201 RP11-143N13.2, ENSG00000260725 AC005307.1, ENSG00000258223 PRSS58, ENSG00000053524 MCF2L2, ENSG00000174992 ZG16, ENSG00000235631 RNF148, ENSG00000244300 RP11-475N22.4, ENSG00000260464 RP4-561L24.3, ENSG00000268107 AC003005.4, ENSG00000258810 RP11-219E7.1, ENSG00000173431 RNASE8, ENSG00000174807 CD248, ENSG00000267259 CTD-2008P7.9, ENSG00000273281 RP11-339B21.14, ENSG00000170921 TANC2, ENSG00000229084 LINC00226, ENSG00000253644 KB-1930G5.3, ENSG00000272656 RP11-219D15.3, ENSG00000121742 GJB6, ENSG00000253392 AC006277.2, ENSG00000238004 AC009227.3, ENSG00000267607 CTD-2369P2.8, ENSG00000255322 RP11-22P4.1, ENSG00000205622 AF064858.6, ENSG00000151388 ADAMTS12, ENSG00000224739 AC016735.1, ENSG00000242104 RP11-340E6.1, ENSG00000250337 LINC01021, ENSG00000259437 RP11-798K3.4, ENSG00000228526 RP3-510D11.1, ENSG00000162711 NLRP3, ENSG00000155719 OTOA, ENSG00000257787 RP11-20L19.1, ENSG00000160505 NLRP4, ENSG00000235586 AC011247.3, ENSG00000258926 RP11-47I22.1, ENSG00000126785 RHOJ, ENSG00000159556 ISL2, ENSG00000253524 RP11-89M20.2, ENSG00000272817 RP11-402D21.2, ENSG00000225265 RP11-378J18.3, ENSG00000258867 LINC01146, ENSG00000168246 UBTD2, ENSG00000259364 RP11-64K12.9, ENSG00000168903 BTNL3, ENSG00000179941 BBS10, ENSG00000100068 LRP5L, ENSG00000250234 CTD-2024P10.1, ENSG00000232183 RP6-27P15.2, ENSG00000258455 RP11-665C16.5, ENSG00000267552 CTD-2528L19.4, ENSG00000120094 HOXB1, ENSG00000176358 TAC4, ENSG00000273104 CMP21-97G8.1, ENSG00000254902 ANO1-AS1, ENSG00000101435 CST9L, ENSG00000254187 CTB-78F1.1, ENSG00000248864 RP11-348J24.1, ENSG00000184985 SORCS2, ENSG00000204481 PRAMEF14, ENSG00000235772 AP001625.6, ENSG00000267070 RP11-10K17.6, ENSG00000272040 CTC-366B18.4, ENSG00000158859 ADAMTS4, ENSG00000234551 RP11-123H22.1, ENSG00000231297 SNORD45, ENSG00000118972 FGF23, ENSG00000229272 RP11-498J9.2, ENSG00000177822 AC108142.1, ENSG00000106299 WASL, ENSG00000133115 STOML3, ENSG00000236544 AC008060.8, ENSG00000134871 COL4A2, ENSG00000166869 CHP2, ENSG00000173401 GLIPR1L1, ENSG00000162757 C1orf74, ENSG00000225194 LINC00092, ENSG00000189266 PNRC2, ENSG00000261194 RP11-704C2.1, ENSG00000255355 AP000640.2, ENSG00000267838 AC008746.12, ENSG00000215549 AL138815.1, ENSG00000187612 OR5W2, ENSG00000238042 RP11-815M8.1, ENSG00000269709 AL109659.1, ENSG00000177476 OR2G3, ENSG00000188859 FAM78B, ENSG00000228302 RP11-186N15.3, ENSG00000272962 SLC5A3, ENSG00000257523 CTD-2384A14.2, ENSG00000237189 RP11-85G21.2, ENSG00000261020 RP11-744K17.1, ENSG00000226516 FAM138B, ENSG00000260977 RP11-333I13.1, ENSG00000241732 RP11-38P22.2, ENSG0000025
#> PC_ 1
#> Positive: ENSG00000122026 RPL21, ENSG00000063177 RPL18, ENSG00000162244 RPL29, ENSG00000105373 GLTSCR2, ENSG00000105193 RPS16, ENSG00000165983 PTER, ENSG00000145416 MARCH1, ENSG00000073614 KDM5A, ENSG00000109787 KLF3, ENSG00000167483 FAM129C
#> ENSG00000115947 ORC4, ENSG00000084234 APLP2, ENSG00000130787 HIP1R, ENSG00000262202 SNORD3D, ENSG00000175155 YPEL2, ENSG00000267680 ZNF224, ENSG00000271858 XXcos-LUCA11.4, ENSG00000214900 C14orf182, ENSG00000163728 TTC14, ENSG00000145439 CBR4
#> ENSG00000272269 RP11-500C11.3, ENSG00000204482 LST1, ENSG00000172216 CEBPB, ENSG00000186166 CCDC84, ENSG00000118518 RNF146, ENSG00000085982 USP40, ENSG00000257698 RP11-620J15.3, ENSG00000173933 RBM4, ENSG00000204252 HLA-DOA, ENSG00000157106 SMG1
#> Negative: ENSG00000166387 PPFIBP2, ENSG00000124787 RPP40, ENSG00000082641 NFE2L1, ENSG00000143228 NUF2, ENSG00000253426 RP11-10A14.4, ENSG00000169679 BUB1, ENSG00000111206 FOXM1, ENSG00000155324 GRAMD3, ENSG00000167513 CDT1, ENSG00000152253 SPC25
#> ENSG00000072571 HMMR, ENSG00000157456 CCNB2, ENSG00000257303 RP11-977G19.11, ENSG00000163467 TSACC, ENSG00000186376 ZNF75D, ENSG00000102575 ACP5, ENSG00000123240 OPTN, ENSG00000139193 CD27, ENSG00000125817 CENPB, ENSG00000134014 ELP3
#> ENSG00000106683 LIMK1, ENSG00000173457 PPP1R14B, ENSG00000197157 SND1, ENSG00000108010 GLRX3, ENSG00000213977 TAX1BP3, ENSG00000260083 MIR4519, ENSG00000167136 ENDOG, ENSG00000030582 GRN, ENSG00000196505 GDAP2, ENSG00000158481 CD1C
#> PC_ 2
#> Positive: ENSG00000223865 HLA-DPB1, ENSG00000158481 CD1C, ENSG00000239961 LILRA4, ENSG00000112799 LY86, ENSG00000099956 SMARCB1, ENSG00000166228 PCBD1, ENSG00000161091 MFSD12, ENSG00000172366 FAM195A, ENSG00000125726 CD70, ENSG00000163156 SCNM1
#> ENSG00000148719 DNAJB12, ENSG00000012779 ALOX5, ENSG00000173559 NABP1, ENSG00000127481 UBR4, ENSG00000072694 FCGR2B, ENSG00000107581 EIF3A, ENSG00000213240 NOTCH2NL, ENSG00000102575 ACP5, ENSG00000066336 SPI1, ENSG00000175893 ZDHHC21
#> ENSG00000099330 OCEL1, ENSG00000108588 CCDC47, ENSG00000129534 MIS18BP1, ENSG00000134884 ARGLU1, ENSG00000080189 SLC35C2, ENSG00000076685 NT5C2, ENSG00000112159 MDN1, ENSG00000185347 C14orf80, ENSG00000174004 NRROS, ENSG00000155657 TTN
#> Negative: ENSG00000090554 FLT3LG, ENSG00000122026 RPL21, ENSG00000168209 DDIT4, ENSG00000125817 CENPB, ENSG00000197880 MDS2, ENSG00000082641 NFE2L1, ENSG00000198821 CD247, ENSG00000154764 WNT7A, ENSG00000253426 RP11-10A14.4, ENSG00000168496 FEN1
#> ENSG00000163467 TSACC, ENSG00000153130 SCOC, ENSG00000160087 UBE2J2, ENSG00000066739 ATG2B, ENSG00000027075 PRKCH, ENSG00000148950 IMMP1L, ENSG00000143228 NUF2, ENSG00000169679 BUB1, ENSG00000111206 FOXM1, ENSG00000072571 HMMR
#> ENSG00000152253 SPC25, ENSG00000167513 CDT1, ENSG00000157456 CCNB2, ENSG00000155324 GRAMD3, ENSG00000186376 ZNF75D, ENSG00000257303 RP11-977G19.11, ENSG00000122971 ACADS, ENSG00000238227 C9orf69, ENSG00000120915 EPHX2, ENSG00000172216 CEBPB
#> PC_ 3
#> Positive: ENSG00000198821 CD247, ENSG00000139193 CD27, ENSG00000090554 FLT3LG, ENSG00000159496 RGL4, ENSG00000168209 DDIT4, ENSG00000166971 AKTIP, ENSG00000027075 PRKCH, ENSG00000101474 APMAP, ENSG00000129932 DOHH, ENSG00000173221 GLRX
#> ENSG00000111348 ARHGDIB, ENSG00000137193 PIM1, ENSG00000187118 CMC1, ENSG00000180096 SEPT1, ENSG00000167815 PRDX2, ENSG00000172757 CFL1, ENSG00000160888 IER2, ENSG00000141522 ARHGDIA, ENSG00000099330 OCEL1, ENSG00000235999 RP11-403I13.8
#> ENSG00000026025 VIM, ENSG00000109046 WSB1, ENSG00000109062 SLC9A3R1, ENSG00000167118 URM1, ENSG00000118680 MYL12B, ENSG00000120915 EPHX2, ENSG00000108010 GLRX3, ENSG00000141101 NOB1, ENSG00000273080 RP11-301O19.1, ENSG00000100129 EIF3L
#> Negative: ENSG00000223865 HLA-DPB1, ENSG00000257303 RP11-977G19.11, ENSG00000100908 EMC9, ENSG00000186376 ZNF75D, ENSG00000143228 NUF2, ENSG00000253426 RP11-10A14.4, ENSG00000163467 TSACC, ENSG00000082641 NFE2L1, ENSG00000173457 PPP1R14B, ENSG00000111206 FOXM1
#> ENSG00000157456 CCNB2, ENSG00000072571 HMMR, ENSG00000167513 CDT1, ENSG00000155324 GRAMD3, ENSG00000152253 SPC25, ENSG00000169679 BUB1, ENSG00000196505 GDAP2, ENSG00000148840 PPRC1, ENSG00000128039 SRD5A3, ENSG00000111224 PARP11
#> ENSG00000112799 LY86, ENSG00000156313 RPGR, ENSG00000166387 PPFIBP2, ENSG00000165733 BMS1, ENSG00000227039 ITGB2-AS1, ENSG00000126391 FRMD8, ENSG00000247240 UBL7-AS1, ENSG00000160741 CRTC2, ENSG00000106683 LIMK1, ENSG00000205155 PSENEN
#> PC_ 4
#> Positive: ENSG00000149929 HIRIP3, ENSG00000233937 CTC-338M12.4, ENSG00000153896 ZNF599, ENSG00000167208 SNX20, ENSG00000135913 USP37, ENSG00000237438 CECR7, ENSG00000004468 CD38, ENSG00000095319 NUP188, ENSG00000271856 RP11-861A13.4, ENSG00000121064 SCPEP1
#> ENSG00000225828 FAM229A, ENSG00000273080 RP11-301O19.1, ENSG00000079246 XRCC5, ENSG00000196642 RABL6, ENSG00000168818 STX18, ENSG00000196230 TUBB, ENSG00000124357 NAGK, ENSG00000159753 RLTPR, ENSG00000112159 MDN1, ENSG00000180957 PITPNB
#> ENSG00000197989 SNHG12, ENSG00000003249 DBNDD1, ENSG00000196262 PPIA, ENSG00000080189 SLC35C2, ENSG00000064651 SLC12A2, ENSG00000132424 PNISR, ENSG00000128191 DGCR8, ENSG00000198355 PIM3, ENSG00000211456 SACM1L, ENSG00000100416 TRMU
#> Negative: ENSG00000170175 CHRNB1, ENSG00000126368 NR1D1, ENSG00000112640 PPP2R5D, ENSG00000154764 WNT7A, ENSG00000054148 PHPT1, ENSG00000105329 TGFB1, ENSG00000120915 EPHX2, ENSG00000134460 IL2RA, ENSG00000110330 BIRC2, ENSG00000153201 RANBP2
#> ENSG00000020256 ZFP64, ENSG00000120948 TARDBP, ENSG00000163564 PYHIN1, ENSG00000127527 EPS15L1, ENSG00000168806 LCMT2, ENSG00000148218 ALAD, ENSG00000173442 EHBP1L1, ENSG00000100083 GGA1, ENSG00000072364 AFF4, ENSG00000158481 CD1C
#> ENSG00000136819 C9orf78, ENSG00000189339 SLC35E2B, ENSG00000198498 TMA16, ENSG00000150776 C11orf57, ENSG00000270170 NCBP2-AS2, ENSG00000150054 MPP7, ENSG00000178773 CPNE7, ENSG00000088766 CRLS1, ENSG00000173559 NABP1, ENSG00000173264 GPR137
#> PC_ 5
#> Positive: ENSG00000173221 GLRX, ENSG00000167196 FBXO22, ENSG00000125995 ROMO1, ENSG00000109534 GAR1, ENSG00000221916 C19orf73, ENSG00000109118 PHF12, ENSG00000167118 URM1, ENSG00000106355 LSM5, ENSG00000139921 TMX1, ENSG00000173559 NABP1
#> ENSG00000241990 RP6-109B7.3, ENSG00000169905 TOR1AIP2, ENSG00000150776 C11orf57, ENSG00000129932 DOHH, ENSG00000152127 MGAT5, ENSG00000180423 HARBI1, ENSG00000108010 GLRX3, ENSG00000219545 RPA3-AS1, ENSG00000174456 C12orf76, ENSG00000131196 NFATC1
#> ENSG00000156515 HK1, ENSG00000163960 UBXN7, ENSG00000162642 C1orf52, ENSG00000108774 RAB5C, ENSG00000163156 SCNM1, ENSG00000134109 EDEM1, ENSG00000101220 C20orf27, ENSG00000127838 PNKD, ENSG00000236104 ZBTB22, ENSG00000142856 ITGB3BP
#> Negative: ENSG00000229539 RP11-119B16.2, ENSG00000126368 NR1D1, ENSG00000148218 ALAD, ENSG00000145545 SRD5A1, ENSG00000120697 ALG5, ENSG00000109046 WSB1, ENSG00000168818 STX18, ENSG00000112640 PPP2R5D, ENSG00000112096 SOD2, ENSG00000141101 NOB1
#> ENSG00000118900 UBN1, ENSG00000154764 WNT7A, ENSG00000117528 ABCD3, ENSG00000114857 NKTR, ENSG00000198546 ZNF511, ENSG00000171302 CANT1, ENSG00000204954 C12orf73, ENSG00000108826 MRPL27, ENSG00000015479 MATR3, ENSG00000125637 PSD4
#> ENSG00000128524 ATP6V1F, ENSG00000137404 NRM, ENSG00000132549 VPS13B, ENSG00000174886 NDUFA11, ENSG00000115128 SF3B14, ENSG00000153814 JAZF1, ENSG00000079246 XRCC5, ENSG00000139197 PEX5, ENSG00000054148 PHPT1, ENSG00000096968 JAK2
#> 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: 21610
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.5099
#> Number of communities: 2
#> Elapsed time: 0 seconds
#> Normalizing layer: counts
#> Finding variable features for layer counts
#> Warning: pseudoinverse used at -2.1491
#> Warning: neighborhood radius 0.3166
#> Warning: reciprocal condition number 0
#> Warning: There are other near singularities as well. 0.031008
#> Centering and scaling data matrix
#> Warning: The following 1117 features requested have zero variance; running reduction without them: ENSG00000172733 PURG, ENSG00000174529 TMEM81, ENSG00000180209 MYLPF, ENSG00000261231 RP11-523L20.2, ENSG00000189367 KIAA0408, ENSG00000086570 FAT2, ENSG00000249882 RP11-665I14.1, ENSG00000237853 RP5-833A20.1, ENSG00000228857 AC104653.1, ENSG00000255276 RRM1-AS1, ENSG00000224902 GAGE12H, ENSG00000164185 ZNF474, ENSG00000248703 RP11-495K9.3, ENSG00000251151 HOXC-AS3, ENSG00000177076 ACER2, ENSG00000134014 ELP3, ENSG00000267038 RP11-1096D5.2, ENSG00000228569 AC073133.2, ENSG00000260780 RP11-580I1.1, ENSG00000231703 RP4-669H2.1, ENSG00000224658 RP11-631F7.1, ENSG00000250431 RP13-577H12.2, ENSG00000169398 PTK2, ENSG00000231731 AC010976.2, ENSG00000255420 RP11-236J17.3, ENSG00000204889 KRT40, ENSG00000237907 RP5-1013A22.2, ENSG00000185792 NLRP9, ENSG00000272579 RP11-101E13.5, ENSG00000272121 RP4-555D20.4, ENSG00000196754 S100A2, ENSG00000169679 BUB1, ENSG00000251532 CTD-2245E15.3, ENSG00000125954 CHURC1-FNTB, ENSG00000168621 GDNF, ENSG00000224844 AC107079.1, ENSG00000139988 RDH12, ENSG00000132693 CRP, ENSG00000174032 SLC25A30, ENSG00000257985 RP1-228P16.4, ENSG00000261583 CTD-2385L22.1, ENSG00000172260 NEGR1, ENSG00000230687 RP5-1114G22.2, ENSG00000261789 RP11-709D24.5, ENSG00000065320 NTN1, ENSG00000267467 APOC4, ENSG00000006788 MYH13, ENSG00000234622 RP13-297E16.5, ENSG00000233234 RP11-740P5.2, ENSG00000269064 AL160286.1, ENSG00000269895 AP000654.4, ENSG00000267580 CTD-2540B15.11, ENSG00000265778 RP11-17M16.2, ENSG00000269199 AC003973.5, ENSG00000184492 FOXD4L1, ENSG00000185305 ARL15, ENSG00000249847 RP11-192C21.2, ENSG00000226113 RP11-672F9.1, ENSG00000255104 ZNF286A, ENSG00000214960 ISPD, ENSG00000230424 RP1-43E13.2, ENSG00000064309 CDON, ENSG00000254290 RP11-150O12.3, ENSG00000104490 NCALD, ENSG00000261717 RP11-77K12.1, ENSG00000184454 NCMAP, ENSG00000228539 RP11-526K17.2, ENSG00000255062 RP11-712L6.5, ENSG00000236306 RP11-33G16.1, ENSG00000099364 FBXL19, ENSG00000204187 LINC00619, ENSG00000120436 GPR31, ENSG00000178199 ZC3H12D, ENSG00000227131 RP11-552E20.1, ENSG00000245385 RP11-334E6.10, ENSG00000133131 MORC4, ENSG00000175322 ZNF519, ENSG00000242767 ZBTB20-AS4, ENSG00000074696 PTPLAD1, ENSG00000226386 PARD3-AS1, ENSG00000165309 ARMC3, ENSG00000170835 CEL, ENSG00000256391 SDIM1, ENSG00000232530 RP1-102K2.6, ENSG00000115904 SOS1, ENSG00000235910 APOA1-AS, ENSG00000185894 BPY2C, ENSG00000198400 NTRK1, ENSG00000258888 RP11-326A13.1, ENSG00000235085 AC091153.4, ENSG00000198799 LRIG2, ENSG00000204702 OR2J1, ENSG00000156313 RPGR, ENSG00000197937 ZNF347, ENSG00000165996 PTPLA, ENSG00000203301 AL590822.1, ENSG00000178412 RP11-567M16.3, ENSG00000233835 RP1-92C4.2, ENSG00000268012 AC016559.1, ENSG00000268549 RP11-295P9.8, ENSG00000175121 WFDC5, ENSG00000259063 DUX4L5, ENSG00000228213 NLGN1-AS1, ENSG00000233821 ENOX1-AS1, ENSG00000139514 SLC7A1, ENSG00000221938 OR2A14, ENSG00000091128 LAMB4, ENSG00000224691 GS1-174L6.4, ENSG00000183032 SLC25A21, ENSG00000259312 RP11-522B15.5, ENSG00000263335 AF001548.5, ENSG00000270755 RP11-138E2.1, ENSG00000145198 VWA5B2, ENSG00000174111 SOCS7, ENSG00000100012 SEC14L3, ENSG00000181074 OR52N4, ENSG00000250241 RP11-9G1.3, ENSG00000236761 CTAGE9, ENSG00000103528 SYT17, ENSG00000248828 RP11-673E1.4, ENSG00000077458 FAM76B, ENSG00000204110 RP1-153P14.8, ENSG00000227518 MIR1302-9, ENSG00000224201 PNMA6A, ENSG00000225216 AC007362.3, ENSG00000251258 RFPL4B, ENSG00000249639 CTB-138E5.1, ENSG00000156486 KCNS2, ENSG00000228272 AC106874.1, ENSG00000163914 RHO, ENSG00000196532 HIST1H3C, ENSG00000256802 RP11-680F8.1, ENSG00000134853 PDGFRA, ENSG00000117479 SLC19A2, ENSG00000228214 LINC00693, ENSG00000205537 RP11-89H19.1, ENSG00000272663 RP11-191L17.1, ENSG00000229855 CTC-546K23.1, ENSG00000236463 LINC00427, ENSG00000238058 RP11-432J22.2, ENSG00000259044 RP11-789A21.1, ENSG00000268091 AC078925.1, ENSG00000254768 CTD-2140G10.2, ENSG00000130684 ZNF337, ENSG00000125257 ABCC4, ENSG00000268126 AC091948.1, ENSG00000272762 RP11-155D18.14, ENSG00000164236 ANKRD33B, ENSG00000123243 ITIH5, ENSG00000165066 NKX6-3, ENSG00000172382 PRSS27, ENSG00000232529 RP1-257I9.2, ENSG00000231734 RP6-206I17.2, ENSG00000222030 AC007131.1, ENSG00000203364 RP11-370F5.4, ENSG00000240553 RP1-184J9.2, ENSG00000099812 MISP, ENSG00000253893 FAM85B, ENSG00000176742 OR51V1, ENSG00000233244 CYP4F59P, ENSG00000259518 RP11-597K23.2, ENSG00000069764 PLA2G10, ENSG00000253735 RP11-115J16.3, ENSG00000230920 RP11-527D15.1, ENSG00000262576 PCDHGA4, ENSG00000130433 CACNG6, ENSG00000140993 TIGD7, ENSG00000004776 HSPB6, ENSG00000205693 MANSC4, ENSG00000273091 AP000255.6, ENSG00000170549 IRX1, ENSG00000261272 MUC22, ENSG00000172046 USP19, ENSG00000227782 AC002553.1, ENSG00000115602 IL1RL1, ENSG00000176754 LINC00303, ENSG00000131480 AOC2, ENSG00000140798 ABCC12, ENSG00000164855 TMEM184A, ENSG00000233670 PIRT, ENSG00000095319 NUP188, ENSG00000007171 NOS2, ENSG00000226957 RP4-533D7.4, ENSG00000152969 JAKMIP1, ENSG00000187730 GABRD, ENSG00000255327 RP11-555G19.1, ENSG00000099377 HSD3B7, ENSG00000267769 CTB-50L17.9, ENSG00000227047 AC012065.4, ENSG00000206043 C18orf63, ENSG00000165985 C1QL3, ENSG00000231394 RP11-310H4.3, ENSG00000226209 AL138764.1, ENSG00000267191 RP11-15A1.2, ENSG00000198812 LRRC10, ENSG00000186376 ZNF75D, ENSG00000255313 RP11-1082L8.2, ENSG00000268809 AC012360.2, ENSG00000231426 RP5-899B16.1, ENSG00000224616 RP11-305E17.6, ENSG00000259714 LINC00594, ENSG00000254084 KB-1930G5.4, ENSG00000246331 RP11-77I22.2, ENSG00000130701 RBBP8NL, ENSG00000269676 MUC8, ENSG00000268472 AP002884.2, ENSG00000268923 AL645922.1, ENSG00000139797 RNF113B, ENSG00000171540 OTP, ENSG00000257918 RP11-482D24.3, ENSG00000256209 RP11-897M7.1, ENSG00000257894 RP1-78O14.1, ENSG00000264750 RP11-277J6.2, ENSG00000228696 ARL17B, ENSG00000130822 PNCK, ENSG00000058085 LAMC2, ENSG00000243224 RP5-1157M23.2, ENSG00000167858 TEKT1, ENSG00000260235 CTD-2026K11.3, ENSG00000271973 RP11-572O6.1, ENSG00000232080 XXbac-BPG254F23.7, ENSG00000231171 LINC01098, ENSG00000226310 RP3-323P24.3, ENSG00000225872 AC002398.5, ENSG00000260201 RP11-143N13.2, ENSG00000260725 AC005307.1, ENSG00000155657 TTN, ENSG00000232386 RP11-66B24.2, ENSG00000258223 PRSS58, ENSG00000143228 NUF2, ENSG00000053524 MCF2L2, ENSG00000174992 ZG16, ENSG00000235631 RNF148, ENSG00000244300 RP11-475N22.4, ENSG00000178163 ZNF518B, ENSG00000260464 RP4-561L24.3, ENSG00000145908 ZNF300, ENSG00000268107 AC003005.4, ENSG00000258810 RP11-219E7.1, ENSG00000173431 RNASE8, ENSG00000174807 CD248, ENSG00000267259 CTD-2008P7.9, ENSG00000273281 RP11-339B21.14, ENSG00000253644 KB-1930G5.3, ENSG00000272656 RP11-219D15.3, ENSG00000121742 GJB6, ENSG00000253392 AC006277.2, ENSG00000072121 ZFYVE26, ENSG00000238004 AC009227.3, ENSG00000267607 CTD-2369P2.8, ENSG00000255322 RP11-22P4.1, ENSG00000205622 AF064858.6, ENSG00000235192 AC009495.2, ENSG00000151388 ADAMTS12, ENSG00000224739 AC016735.1, ENSG00000242104 RP11-340E6.1, ENSG00000250337 LINC01021, ENSG00000259437 RP11-798K3.4, ENSG00000228526 RP3-510D11.1, ENSG00000155719 OTOA, ENSG00000257787 RP11-20L19.1, ENSG00000160505 NLRP4, ENSG00000114455 HHLA2, ENSG00000235586 AC011247.3, ENSG00000258926 RP11-47I22.1, ENSG00000126785 RHOJ, ENSG00000253524 RP11-89M20.2, ENSG00000272817 RP11-402D21.2, ENSG00000258867 LINC01146, ENSG00000168246 UBTD2, ENSG00000259364 RP11-64K12.9, ENSG00000168903 BTNL3, ENSG00000179941 BBS10, ENSG00000198551 ZNF627, ENSG00000250234 CTD-2024P10.1, ENSG00000232183 RP6-27P15.2, ENSG00000258455 RP11-665C16.5, ENSG00000267552 CTD-2528L19.4, ENSG00000120094 HOXB1, ENSG00000176358 TAC4, ENSG00000273104 CMP21-97G8.1, ENSG00000254902 ANO1-AS1, ENSG00000101435 CST9L, ENSG00000173786 CNP, ENSG00000254187 CTB-78F1.1, ENSG00000248864 RP11-348J24.1, ENSG00000184985 SORCS2, ENSG00000204481 PRAMEF14, ENSG00000235772 AP001625.6, ENSG00000267070 RP11-10K17.6, ENSG00000272040 CTC-366B18.4, ENSG00000158859 ADAMTS4, ENSG00000234551 RP11-123H22.1, ENSG00000231297 SNORD45, ENSG00000118972 FGF23, ENSG00000229272 RP11-498J9.2, ENSG00000177822 AC108142.1, ENSG00000106299 WASL, ENSG00000133115 STOML3, ENSG00000236544 AC008060.8, ENSG00000134871 COL4A2, ENSG00000166869 CHP2, ENSG00000173401 GLIPR1L1, ENSG00000162757 C1orf74, ENSG00
#> PC_ 1
#> Positive: ENSG00000063177 RPL18, ENSG00000122026 RPL21, ENSG00000198821 CD247, ENSG00000144746 ARL6IP5, ENSG00000139193 CD27, ENSG00000123240 OPTN, ENSG00000027075 PRKCH, ENSG00000260083 MIR4519, ENSG00000088766 CRLS1, ENSG00000090554 FLT3LG
#> ENSG00000161204 ABCF3, ENSG00000154473 BUB3, ENSG00000090447 TFAP4, ENSG00000132382 MYBBP1A, ENSG00000155438 NIFK, ENSG00000176248 ANAPC2, ENSG00000105373 GLTSCR2, ENSG00000099917 MED15, ENSG00000016864 GLT8D1, ENSG00000154764 WNT7A
#> ENSG00000120915 EPHX2, ENSG00000149311 ATM, ENSG00000189339 SLC35E2B, ENSG00000224051 GLTPD1, ENSG00000109920 FNBP4, ENSG00000166971 AKTIP, ENSG00000126749 EMG1, ENSG00000140545 MFGE8, ENSG00000105193 RPS16, ENSG00000124787 RPP40
#> Negative: ENSG00000197780 TAF13, ENSG00000204388 HSPA1B, ENSG00000135093 USP30, ENSG00000164305 CASP3, ENSG00000167196 FBXO22, ENSG00000085788 DDHD2, ENSG00000186522 SEPT10, ENSG00000171848 RRM2, ENSG00000119411 BSPRY, ENSG00000071655 MBD3
#> ENSG00000156170 NDUFAF6, ENSG00000130787 HIP1R, ENSG00000118292 C1orf54, ENSG00000119782 FKBP1B, ENSG00000140691 ARMC5, ENSG00000182359 KBTBD3, ENSG00000100368 CSF2RB, ENSG00000223865 HLA-DPB1, ENSG00000139921 TMX1, ENSG00000075234 TTC38
#> ENSG00000066336 SPI1, ENSG00000173064 HECTD4, ENSG00000140263 SORD, ENSG00000030582 GRN, ENSG00000213246 SUPT4H1, ENSG00000197816 CCDC180, ENSG00000166145 SPINT1, ENSG00000166224 SGPL1, ENSG00000130714 POMT1, ENSG00000117899 MESDC2
#> PC_ 2
#> Positive: ENSG00000223865 HLA-DPB1, ENSG00000112799 LY86, ENSG00000066336 SPI1, ENSG00000204482 LST1, ENSG00000118292 C1orf54, ENSG00000025708 TYMP, ENSG00000030582 GRN, ENSG00000161243 FBXO27, ENSG00000166736 HTR3A, ENSG00000146757 ZNF92
#> ENSG00000166145 SPINT1, ENSG00000119782 FKBP1B, ENSG00000092036 HAUS4, ENSG00000139278 GLIPR1, ENSG00000198951 NAGA, ENSG00000124570 SERPINB6, ENSG00000101220 C20orf27, ENSG00000163131 CTSS, ENSG00000140263 SORD, ENSG00000126759 CFP
#> ENSG00000124357 NAGK, ENSG00000115204 MPV17, ENSG00000139921 TMX1, ENSG00000155366 RHOC, ENSG00000130475 FCHO1, ENSG00000100908 EMC9, ENSG00000155330 C16orf87, ENSG00000168303 MPLKIP, ENSG00000128524 ATP6V1F, ENSG00000123908 AGO2
#> Negative: ENSG00000171848 RRM2, ENSG00000071655 MBD3, ENSG00000156170 NDUFAF6, ENSG00000130787 HIP1R, ENSG00000167196 FBXO22, ENSG00000186522 SEPT10, ENSG00000085788 DDHD2, ENSG00000204388 HSPA1B, ENSG00000119411 BSPRY, ENSG00000197780 TAF13
#> ENSG00000135093 USP30, ENSG00000164305 CASP3, ENSG00000160113 NR2F6, ENSG00000184451 CCR10, ENSG00000150347 ARID5B, ENSG00000197816 CCDC180, ENSG00000100368 CSF2RB, ENSG00000075234 TTC38, ENSG00000055163 CYFIP2, ENSG00000128829 EIF2AK4
#> ENSG00000134285 FKBP11, ENSG00000139193 CD27, ENSG00000103353 UBFD1, ENSG00000108349 CASC3, ENSG00000004468 CD38, ENSG00000090554 FLT3LG, ENSG00000180096 SEPT1, ENSG00000100124 ANKRD54, ENSG00000130714 POMT1, ENSG00000115806 GORASP2
#> PC_ 3
#> Positive: ENSG00000269996 RP11-343N15.5, ENSG00000048991 R3HDM1, ENSG00000167483 FAM129C, ENSG00000183018 SPNS2, ENSG00000177398 UMODL1, ENSG00000107447 DNTT, ENSG00000263508 RP11-963H4.3, ENSG00000214367 HAUS3, ENSG00000174059 CD34, ENSG00000229084 LINC00226
#> ENSG00000175893 ZDHHC21, ENSG00000032742 IFT88, ENSG00000184708 EIF4ENIF1, ENSG00000159753 RLTPR, ENSG00000185291 IL3RA, ENSG00000121931 LRIF1, ENSG00000138138 ATAD1, ENSG00000256060 TRAPPC2P1, ENSG00000215039 CD27-AS1, ENSG00000082641 NFE2L1
#> ENSG00000145687 SSBP2, ENSG00000106608 URGCP, ENSG00000115289 PCGF1, ENSG00000155252 PI4K2A, ENSG00000143570 SLC39A1, ENSG00000117335 CD46, ENSG00000251022 THAP9-AS1, ENSG00000271858 XXcos-LUCA11.4, ENSG00000148248 SURF4, ENSG00000148719 DNAJB12
#> Negative: ENSG00000025708 TYMP, ENSG00000229117 RPL41, ENSG00000163131 CTSS, ENSG00000030582 GRN, ENSG00000112799 LY86, ENSG00000134072 CAMK1, ENSG00000120742 SERP1, ENSG00000164733 CTSB, ENSG00000026025 VIM, ENSG00000174886 NDUFA11
#> ENSG00000186010 NDUFA13, ENSG00000182578 CSF1R, ENSG00000172216 CEBPB, ENSG00000173221 GLRX, ENSG00000075234 TTC38, ENSG00000223865 HLA-DPB1, ENSG00000124357 NAGK, ENSG00000108826 MRPL27, ENSG00000119705 SLIRP, ENSG00000108349 CASC3
#> ENSG00000172757 CFL1, ENSG00000204482 LST1, ENSG00000177663 IL17RA, ENSG00000185507 IRF7, ENSG00000136152 COG3, ENSG00000164305 CASP3, ENSG00000186522 SEPT10, ENSG00000085788 DDHD2, ENSG00000135093 USP30, ENSG00000130787 HIP1R
#> PC_ 4
#> Positive: ENSG00000204482 LST1, ENSG00000025708 TYMP, ENSG00000126759 CFP, ENSG00000223865 HLA-DPB1, ENSG00000163131 CTSS, ENSG00000066336 SPI1, ENSG00000134072 CAMK1, ENSG00000167851 CD300A, ENSG00000136867 SLC31A2, ENSG00000128524 ATP6V1F
#> ENSG00000030582 GRN, ENSG00000159753 RLTPR, ENSG00000184708 EIF4ENIF1, ENSG00000172216 CEBPB, ENSG00000121064 SCPEP1, ENSG00000102524 TNFSF13B, ENSG00000272831 RP11-792A8.4, ENSG00000119705 SLIRP, ENSG00000115233 PSMD14, ENSG00000182578 CSF1R
#> ENSG00000158481 CD1C, ENSG00000173442 EHBP1L1, ENSG00000229117 RPL41, ENSG00000196642 RABL6, ENSG00000249222 ATP5L2, ENSG00000106003 LFNG, ENSG00000124357 NAGK, ENSG00000099956 SMARCB1, ENSG00000267519 MIR24-2, ENSG00000136152 COG3
#> Negative: ENSG00000136717 BIN1, ENSG00000100129 EIF3L, ENSG00000146757 ZNF92, ENSG00000161243 FBXO27, ENSG00000166736 HTR3A, ENSG00000139193 CD27, ENSG00000140263 SORD, ENSG00000105373 GLTSCR2, ENSG00000119782 FKBP1B, ENSG00000133250 ZNF414
#> ENSG00000118292 C1orf54, ENSG00000115042 FAHD2A, ENSG00000111348 ARHGDIB, ENSG00000198821 CD247, ENSG00000122026 RPL21, ENSG00000183431 SF3A3, ENSG00000164327 RICTOR, ENSG00000145741 BTF3, ENSG00000090554 FLT3LG, ENSG00000162244 RPL29
#> ENSG00000164088 PPM1M, ENSG00000139921 TMX1, ENSG00000171148 TADA3, ENSG00000136819 C9orf78, ENSG00000015479 MATR3, ENSG00000184986 TMEM121, ENSG00000169981 ZNF35, ENSG00000123908 AGO2, ENSG00000114923 SLC4A3, ENSG00000135392 DNAJC14
#> PC_ 5
#> Positive: ENSG00000166736 HTR3A, ENSG00000146757 ZNF92, ENSG00000161243 FBXO27, ENSG00000135392 DNAJC14, ENSG00000114923 SLC4A3, ENSG00000168283 BMI1, ENSG00000123908 AGO2, ENSG00000169981 ZNF35, ENSG00000166145 SPINT1, ENSG00000164327 RICTOR
#> ENSG00000092036 HAUS4, ENSG00000129521 EGLN3, ENSG00000170921 TANC2, ENSG00000247240 UBL7-AS1, ENSG00000087076 HSD17B14, ENSG00000238227 C9orf69, ENSG00000128039 SRD5A3, ENSG00000143797 MBOAT2, ENSG00000100983 GSS, ENSG00000126821 SGPP1
#> ENSG00000131368 MRPS25, ENSG00000155330 C16orf87, ENSG00000120868 APAF1, ENSG00000261737 RP4-612B15.3, ENSG00000184575 XPOT, ENSG00000173559 NABP1, ENSG00000110921 MVK, ENSG00000110367 DDX6, ENSG00000104164 BLOC1S6, ENSG00000214756 METTL12
#> Negative: ENSG00000173064 HECTD4, ENSG00000167536 DHRS13, ENSG00000172831 CES2, ENSG00000106683 LIMK1, ENSG00000080200 CRYBG3, ENSG00000170542 SERPINB9, ENSG00000163040 CCDC74A, ENSG00000100416 TRMU, ENSG00000272269 RP11-500C11.3, ENSG00000236104 ZBTB22
#> ENSG00000150776 C11orf57, ENSG00000004487 KDM1A, ENSG00000198498 TMA16, ENSG00000156876 SASS6, ENSG00000140090 SLC24A4, ENSG00000119782 FKBP1B, ENSG00000146067 FAM193B, ENSG00000254415 SIGLEC14, ENSG00000167522 ANKRD11, ENSG00000125817 CENPB
#> ENSG00000182359 KBTBD3, ENSG00000121644 DESI2, ENSG00000133250 ZNF414, ENSG00000136689 IL1RN, ENSG00000184674 GSTT1, ENSG00000137074 APTX, ENSG00000148719 DNAJB12, ENSG00000140691 ARMC5, ENSG00000131759 RARA, ENSG00000198715 C1orf85
#> 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: 4813
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.7201
#> Number of communities: 2
#> Elapsed time: 0 seconds
#> Normalizing layer: counts
#> Finding variable features for layer counts
#> Warning: pseudoinverse used at -2.5336
#> Warning: neighborhood radius 0.49481
#> Warning: reciprocal condition number 0
#> Warning: There are other near singularities as well. 0.090619
#> Centering and scaling data matrix
#> Warning: The following 971 features requested have zero variance; running reduction without them: ENSG00000172733 PURG, ENSG00000174529 TMEM81, ENSG00000261231 RP11-523L20.2, ENSG00000189367 KIAA0408, ENSG00000086570 FAT2, ENSG00000249882 RP11-665I14.1, ENSG00000237853 RP5-833A20.1, ENSG00000255276 RRM1-AS1, ENSG00000224902 GAGE12H, ENSG00000164185 ZNF474, ENSG00000248703 RP11-495K9.3, ENSG00000251151 HOXC-AS3, ENSG00000177076 ACER2, ENSG00000267038 RP11-1096D5.2, ENSG00000228569 AC073133.2, ENSG00000260780 RP11-580I1.1, ENSG00000231703 RP4-669H2.1, ENSG00000224658 RP11-631F7.1, ENSG00000250431 RP13-577H12.2, ENSG00000169398 PTK2, ENSG00000231731 AC010976.2, ENSG00000255420 RP11-236J17.3, ENSG00000204889 KRT40, ENSG00000237907 RP5-1013A22.2, ENSG00000185792 NLRP9, ENSG00000272579 RP11-101E13.5, ENSG00000272121 RP4-555D20.4, ENSG00000196754 S100A2, ENSG00000169679 BUB1, ENSG00000251532 CTD-2245E15.3, ENSG00000125954 CHURC1-FNTB, ENSG00000168621 GDNF, ENSG00000224844 AC107079.1, ENSG00000139988 RDH12, ENSG00000132693 CRP, ENSG00000174032 SLC25A30, ENSG00000257985 RP1-228P16.4, ENSG00000261583 CTD-2385L22.1, ENSG00000172260 NEGR1, ENSG00000230687 RP5-1114G22.2, ENSG00000261789 RP11-709D24.5, ENSG00000065320 NTN1, ENSG00000267467 APOC4, ENSG00000006788 MYH13, ENSG00000234622 RP13-297E16.5, ENSG00000233234 RP11-740P5.2, ENSG00000269064 AL160286.1, ENSG00000269895 AP000654.4, ENSG00000267580 CTD-2540B15.11, ENSG00000265778 RP11-17M16.2, ENSG00000269199 AC003973.5, ENSG00000184492 FOXD4L1, ENSG00000249847 RP11-192C21.2, ENSG00000226113 RP11-672F9.1, ENSG00000255104 ZNF286A, ENSG00000263508 RP11-963H4.3, ENSG00000231294 AC006994.2, ENSG00000064309 CDON, ENSG00000254290 RP11-150O12.3, ENSG00000261717 RP11-77K12.1, ENSG00000184454 NCMAP, ENSG00000228539 RP11-526K17.2, ENSG00000255062 RP11-712L6.5, ENSG00000236306 RP11-33G16.1, ENSG00000204187 LINC00619, ENSG00000120436 GPR31, ENSG00000227131 RP11-552E20.1, ENSG00000245385 RP11-334E6.10, ENSG00000226386 PARD3-AS1, ENSG00000165309 ARMC3, ENSG00000170835 CEL, ENSG00000256391 SDIM1, ENSG00000232530 RP1-102K2.6, ENSG00000185894 BPY2C, ENSG00000198400 NTRK1, ENSG00000258888 RP11-326A13.1, ENSG00000235085 AC091153.4, ENSG00000204702 OR2J1, ENSG00000163251 FZD5, ENSG00000203301 AL590822.1, ENSG00000178412 RP11-567M16.3, ENSG00000233835 RP1-92C4.2, ENSG00000268012 AC016559.1, ENSG00000204252 HLA-DOA, ENSG00000268549 RP11-295P9.8, ENSG00000175121 WFDC5, ENSG00000259063 DUX4L5, ENSG00000228213 NLGN1-AS1, ENSG00000233821 ENOX1-AS1, ENSG00000139514 SLC7A1, ENSG00000221938 OR2A14, ENSG00000091128 LAMB4, ENSG00000224691 GS1-174L6.4, ENSG00000183032 SLC25A21, ENSG00000259312 RP11-522B15.5, ENSG00000263335 AF001548.5, ENSG00000145198 VWA5B2, ENSG00000174111 SOCS7, ENSG00000100012 SEC14L3, ENSG00000181074 OR52N4, ENSG00000250241 RP11-9G1.3, ENSG00000236761 CTAGE9, ENSG00000103528 SYT17, ENSG00000248828 RP11-673E1.4, ENSG00000204110 RP1-153P14.8, ENSG00000227518 MIR1302-9, ENSG00000224201 PNMA6A, ENSG00000225216 AC007362.3, ENSG00000251258 RFPL4B, ENSG00000249639 CTB-138E5.1, ENSG00000156486 KCNS2, ENSG00000228272 AC106874.1, ENSG00000163914 RHO, ENSG00000196532 HIST1H3C, ENSG00000256802 RP11-680F8.1, ENSG00000134853 PDGFRA, ENSG00000228214 LINC00693, ENSG00000205537 RP11-89H19.1, ENSG00000229855 CTC-546K23.1, ENSG00000236463 LINC00427, ENSG00000238058 RP11-432J22.2, ENSG00000259044 RP11-789A21.1, ENSG00000268091 AC078925.1, ENSG00000254768 CTD-2140G10.2, ENSG00000125257 ABCC4, ENSG00000268126 AC091948.1, ENSG00000272762 RP11-155D18.14, ENSG00000164236 ANKRD33B, ENSG00000165066 NKX6-3, ENSG00000172382 PRSS27, ENSG00000232529 RP1-257I9.2, ENSG00000222030 AC007131.1, ENSG00000203364 RP11-370F5.4, ENSG00000240553 RP1-184J9.2, ENSG00000099812 MISP, ENSG00000253893 FAM85B, ENSG00000176742 OR51V1, ENSG00000259518 RP11-597K23.2, ENSG00000069764 PLA2G10, ENSG00000253735 RP11-115J16.3, ENSG00000230920 RP11-527D15.1, ENSG00000262576 PCDHGA4, ENSG00000130433 CACNG6, ENSG00000004776 HSPB6, ENSG00000205693 MANSC4, ENSG00000273091 AP000255.6, ENSG00000143797 MBOAT2, ENSG00000170549 IRX1, ENSG00000261272 MUC22, ENSG00000227782 AC002553.1, ENSG00000115602 IL1RL1, ENSG00000176754 LINC00303, ENSG00000131480 AOC2, ENSG00000140798 ABCC12, ENSG00000164855 TMEM184A, ENSG00000233670 PIRT, ENSG00000007171 NOS2, ENSG00000226957 RP4-533D7.4, ENSG00000187730 GABRD, ENSG00000259375 RP11-815J21.2, ENSG00000255327 RP11-555G19.1, ENSG00000099377 HSD3B7, ENSG00000267769 CTB-50L17.9, ENSG00000227047 AC012065.4, ENSG00000206043 C18orf63, ENSG00000165985 C1QL3, ENSG00000231394 RP11-310H4.3, ENSG00000226209 AL138764.1, ENSG00000267191 RP11-15A1.2, ENSG00000198812 LRRC10, ENSG00000255313 RP11-1082L8.2, ENSG00000268809 AC012360.2, ENSG00000231426 RP5-899B16.1, ENSG00000224616 RP11-305E17.6, ENSG00000259714 LINC00594, ENSG00000254084 KB-1930G5.4, ENSG00000246331 RP11-77I22.2, ENSG00000130701 RBBP8NL, ENSG00000269676 MUC8, ENSG00000268472 AP002884.2, ENSG00000268923 AL645922.1, ENSG00000139797 RNF113B, ENSG00000171540 OTP, ENSG00000256209 RP11-897M7.1, ENSG00000257894 RP1-78O14.1, ENSG00000182578 CSF1R, ENSG00000264750 RP11-277J6.2, ENSG00000130822 PNCK, ENSG00000058085 LAMC2, ENSG00000167858 TEKT1, ENSG00000260235 CTD-2026K11.3, ENSG00000271973 RP11-572O6.1, ENSG00000232080 XXbac-BPG254F23.7, ENSG00000231171 LINC01098, ENSG00000226310 RP3-323P24.3, ENSG00000225872 AC002398.5, ENSG00000260201 RP11-143N13.2, ENSG00000260725 AC005307.1, ENSG00000155657 TTN, ENSG00000232386 RP11-66B24.2, ENSG00000258223 PRSS58, ENSG00000174992 ZG16, ENSG00000235631 RNF148, ENSG00000244300 RP11-475N22.4, ENSG00000178163 ZNF518B, ENSG00000268107 AC003005.4, ENSG00000258810 RP11-219E7.1, ENSG00000173431 RNASE8, ENSG00000174807 CD248, ENSG00000267259 CTD-2008P7.9, ENSG00000273281 RP11-339B21.14, ENSG00000229084 LINC00226, ENSG00000253644 KB-1930G5.3, ENSG00000254415 SIGLEC14, ENSG00000272656 RP11-219D15.3, ENSG00000121742 GJB6, ENSG00000253392 AC006277.2, ENSG00000238004 AC009227.3, ENSG00000267607 CTD-2369P2.8, ENSG00000255322 RP11-22P4.1, ENSG00000205622 AF064858.6, ENSG00000151388 ADAMTS12, ENSG00000224739 AC016735.1, ENSG00000242104 RP11-340E6.1, ENSG00000250337 LINC01021, ENSG00000259437 RP11-798K3.4, ENSG00000228526 RP3-510D11.1, ENSG00000162711 NLRP3, ENSG00000155719 OTOA, ENSG00000257787 RP11-20L19.1, ENSG00000160505 NLRP4, ENSG00000114455 HHLA2, ENSG00000235586 AC011247.3, ENSG00000258926 RP11-47I22.1, ENSG00000126785 RHOJ, ENSG00000159556 ISL2, ENSG00000253524 RP11-89M20.2, ENSG00000225265 RP11-378J18.3, ENSG00000273314 RP5-1136G13.2, ENSG00000258867 LINC01146, ENSG00000168246 UBTD2, ENSG00000259364 RP11-64K12.9, ENSG00000168903 BTNL3, ENSG00000179941 BBS10, ENSG00000250234 CTD-2024P10.1, ENSG00000232183 RP6-27P15.2, ENSG00000258455 RP11-665C16.5, ENSG00000267552 CTD-2528L19.4, ENSG00000120094 HOXB1, ENSG00000176358 TAC4, ENSG00000273104 CMP21-97G8.1, ENSG00000254902 ANO1-AS1, ENSG00000101435 CST9L, ENSG00000254187 CTB-78F1.1, ENSG00000248864 RP11-348J24.1, ENSG00000184985 SORCS2, ENSG00000204481 PRAMEF14, ENSG00000235772 AP001625.6, ENSG00000267070 RP11-10K17.6, ENSG00000272040 CTC-366B18.4, ENSG00000158859 ADAMTS4, ENSG00000234551 RP11-123H22.1, ENSG00000231297 SNORD45, ENSG00000118972 FGF23, ENSG00000229272 RP11-498J9.2, ENSG00000177822 AC108142.1, ENSG00000106299 WASL, ENSG00000133115 STOML3, ENSG00000236544 AC008060.8, ENSG00000134871 COL4A2, ENSG00000166869 CHP2, ENSG00000173401 GLIPR1L1, ENSG00000162757 C1orf74, ENSG00000261194 RP11-704C2.1, ENSG00000255355 AP000640.2, ENSG00000267838 AC008746.12, ENSG00000215549 AL138815.1, ENSG00000187612 OR5W2, ENSG00000238042 RP11-815M8.1, ENSG00000269709 AL109659.1, ENSG00000177476 OR2G3, ENSG00000188859 FAM78B, ENSG00000228302 RP11-186N15.3, ENSG00000272962 SLC5A3, ENSG00000257523 CTD-2384A14.2, ENSG00000237189 RP11-85G21.2, ENSG00000261020 RP11-744K17.1, ENSG00000226516 FAM138B, ENSG00000260977 RP11-333I13.1, ENSG00000241732 RP11-38P22.2, ENSG00000255618 RP11-357K6.1, ENSG00000134588 USP26, ENSG00000234193 AC097461.4, ENSG00000245870 LINC00682, ENSG00000268842 CTD-2245F17.2, ENSG00000267601 RP11-323N12.5, ENSG00000215635 AC145205.1, ENSG00000240710 RP11-430C7.4, ENSG00000234279 AC113618.1, ENSG00000204001 LCN8, ENSG00000260905
#> PC_ 1
#> Positive: ENSG00000187118 CMC1, ENSG00000198821 CD247, ENSG00000155366 RHOC, ENSG00000156411 C14orf2, ENSG00000168701 TMEM208, ENSG00000075234 TTC38, ENSG00000262202 SNORD3D, ENSG00000167851 CD300A, ENSG00000184007 PTP4A2, ENSG00000125743 SNRPD2
#> ENSG00000186010 NDUFA13, ENSG00000213741 RPS29, ENSG00000099956 SMARCB1, ENSG00000130770 ATPIF1, ENSG00000196262 PPIA, ENSG00000101474 APMAP, ENSG00000119705 SLIRP, ENSG00000141002 TCF25, ENSG00000088986 DYNLL1, ENSG00000198574 SH2D1B
#> ENSG00000170540 ARL6IP1, ENSG00000105058 FAM32A, ENSG00000115053 NCL, ENSG00000108826 MRPL27, ENSG00000139725 RHOF, ENSG00000004468 CD38, ENSG00000122482 ZNF644, ENSG00000184752 NDUFA12, ENSG00000136527 TRA2B, ENSG00000120699 EXOSC8
#> Negative: ENSG00000122026 RPL21, ENSG00000139193 CD27, ENSG00000090554 FLT3LG, ENSG00000120915 EPHX2, ENSG00000162244 RPL29, ENSG00000026025 VIM, ENSG00000135916 ITM2C, ENSG00000100129 EIF3L, ENSG00000105373 GLTSCR2, ENSG00000063177 RPL18
#> ENSG00000139197 PEX5, ENSG00000105193 RPS16, ENSG00000167642 SPINT2, ENSG00000227039 ITGB2-AS1, ENSG00000197880 MDS2, ENSG00000128271 ADORA2A, ENSG00000134202 GSTM3, ENSG00000266947 RP11-799D4.4, ENSG00000159496 RGL4, ENSG00000153391 INO80C
#> ENSG00000232442 CTD-3184A7.4, ENSG00000105443 CYTH2, ENSG00000173327 MAP3K11, ENSG00000154764 WNT7A, ENSG00000121749 TBC1D15, ENSG00000102967 DHODH, ENSG00000095059 DHPS, ENSG00000168209 DDIT4, ENSG00000198355 PIM3, ENSG00000126759 CFP
#> PC_ 2
#> Positive: ENSG00000167136 ENDOG, ENSG00000148218 ALAD, ENSG00000027075 PRKCH, ENSG00000180209 MYLPF, ENSG00000173457 PPP1R14B, ENSG00000109534 GAR1, ENSG00000110367 DDX6, ENSG00000198799 LRIG2, ENSG00000167232 ZNF91, ENSG00000150347 ARID5B
#> ENSG00000121644 DESI2, ENSG00000105829 BET1, ENSG00000224051 GLTPD1, ENSG00000130770 ATPIF1, ENSG00000158828 PINK1, ENSG00000113595 TRIM23, ENSG00000136819 C9orf78, ENSG00000185305 ARL15, ENSG00000213741 RPS29, ENSG00000156411 C14orf2
#> ENSG00000004468 CD38, ENSG00000175756 AURKAIP1, ENSG00000105676 ARMC6, ENSG00000152229 PSTPIP2, ENSG00000185760 KCNQ5, ENSG00000198574 SH2D1B, ENSG00000114416 FXR1, ENSG00000163564 PYHIN1, ENSG00000140987 ZSCAN32, ENSG00000262202 SNORD3D
#> Negative: ENSG00000112640 PPP2R5D, ENSG00000163577 EIF5A2, ENSG00000224597 PTCHD3P1, ENSG00000156853 ZNF689, ENSG00000164305 CASP3, ENSG00000064651 SLC12A2, ENSG00000113391 FAM172A, ENSG00000166260 COX11, ENSG00000169499 PLEKHA2, ENSG00000153767 GTF2E1
#> ENSG00000136152 COG3, ENSG00000134285 FKBP11, ENSG00000153107 ANAPC1, ENSG00000130787 HIP1R, ENSG00000259230 CTD-2555C10.3, ENSG00000185507 IRF7, ENSG00000099942 CRKL, ENSG00000272269 RP11-500C11.3, ENSG00000231889 TRAF3IP2-AS1, ENSG00000102900 NUP93
#> ENSG00000026025 VIM, ENSG00000160781 PAQR6, ENSG00000152193 RNF219, ENSG00000241370 RPP21, ENSG00000124787 RPP40, ENSG00000125637 PSD4, ENSG00000170100 ZNF778, ENSG00000254470 AP5B1, ENSG00000142751 GPN2, ENSG00000156313 RPGR
#> PC_ 3
#> Positive: ENSG00000166228 PCBD1, ENSG00000141522 ARHGDIA, ENSG00000109534 GAR1, ENSG00000123472 ATPAF1, ENSG00000121644 DESI2, ENSG00000013288 MAN2B2, ENSG00000184731 FAM110C, ENSG00000026025 VIM, ENSG00000272269 RP11-500C11.3, ENSG00000110048 OSBP
#> ENSG00000131759 RARA, ENSG00000111666 CHPT1, ENSG00000204856 FAM216A, ENSG00000099991 CABIN1, ENSG00000197223 C1D, ENSG00000174100 MRPL45, ENSG00000165996 PTPLA, ENSG00000136147 PHF11, ENSG00000164327 RICTOR, ENSG00000169905 TOR1AIP2
#> ENSG00000143314 MRPL24, ENSG00000141101 NOB1, ENSG00000120697 ALG5, ENSG00000198498 TMA16, ENSG00000106367 AP1S1, ENSG00000171148 TADA3, ENSG00000122481 RWDD3, ENSG00000148840 PPRC1, ENSG00000253797 UTP14C, ENSG00000167483 FAM129C
#> Negative: ENSG00000139278 GLIPR1, ENSG00000198521 ZNF43, ENSG00000166326 TRIM44, ENSG00000125482 TTF1, ENSG00000224051 GLTPD1, ENSG00000049167 ERCC8, ENSG00000237441 RGL2, ENSG00000113595 TRIM23, ENSG00000143815 LBR, ENSG00000138413 IDH1
#> ENSG00000068745 IP6K2, ENSG00000168818 STX18, ENSG00000004468 CD38, ENSG00000099849 RASSF7, ENSG00000145414 NAF1, ENSG00000075089 ACTR6, ENSG00000204564 C6orf136, ENSG00000153487 ING1, ENSG00000147536 GINS4, ENSG00000164305 CASP3
#> ENSG00000163564 PYHIN1, ENSG00000162959 MEMO1, ENSG00000116906 GNPAT, ENSG00000186017 ZNF566, ENSG00000152229 PSTPIP2, ENSG00000032742 IFT88, ENSG00000260083 MIR4519, ENSG00000134516 DOCK2, ENSG00000153814 JAZF1, ENSG00000180957 PITPNB
#> PC_ 4
#> Positive: ENSG00000273344 PAXIP1-AS1, ENSG00000143167 GPA33, ENSG00000102900 NUP93, ENSG00000108010 GLRX3, ENSG00000128829 EIF2AK4, ENSG00000272269 RP11-500C11.3, ENSG00000092201 SUPT16H, ENSG00000160781 PAQR6, ENSG00000254470 AP5B1, ENSG00000126756 UXT
#> ENSG00000108774 RAB5C, ENSG00000178149 DALRD3, ENSG00000127616 SMARCA4, ENSG00000099942 CRKL, ENSG00000148335 NTMT1, ENSG00000140545 MFGE8, ENSG00000134516 DOCK2, ENSG00000180423 HARBI1, ENSG00000075234 TTC38, ENSG00000267680 ZNF224
#> ENSG00000173933 RBM4, ENSG00000180096 SEPT1, ENSG00000114416 FXR1, ENSG00000132549 VPS13B, ENSG00000168090 COPS6, ENSG00000215014 AL645728.1, ENSG00000262202 SNORD3D, ENSG00000166548 TK2, ENSG00000142856 ITGB3BP, ENSG00000105058 FAM32A
#> Negative: ENSG00000172216 CEBPB, ENSG00000105705 SUGP1, ENSG00000136811 ODF2, ENSG00000150776 C11orf57, ENSG00000071655 MBD3, ENSG00000113595 TRIM23, ENSG00000148218 ALAD, ENSG00000130787 HIP1R, ENSG00000013288 MAN2B2, ENSG00000129534 MIS18BP1
#> ENSG00000228857 AC104653.1, ENSG00000223759 RP11-353N4.4, ENSG00000174456 C12orf76, ENSG00000120699 EXOSC8, ENSG00000174100 MRPL45, ENSG00000153107 ANAPC1, ENSG00000164305 CASP3, ENSG00000167862 ICT1, ENSG00000172831 CES2, ENSG00000184277 TM2D3
#> ENSG00000165359 DDX26B, ENSG00000032742 IFT88, ENSG00000160285 LSS, ENSG00000164306 PRIMPOL, ENSG00000197841 ZNF181, ENSG00000260083 MIR4519, ENSG00000122026 RPL21, ENSG00000116497 S100PBP, ENSG00000224051 GLTPD1, ENSG00000135521 LTV1
#> PC_ 5
#> Positive: ENSG00000180376 CCDC66, ENSG00000121064 SCPEP1, ENSG00000137404 NRM, ENSG00000165671 NSD1, ENSG00000166133 RPUSD2, ENSG00000141002 TCF25, ENSG00000120948 TARDBP, ENSG00000174886 NDUFA11, ENSG00000105373 GLTSCR2, ENSG00000126749 EMG1
#> ENSG00000221916 C19orf73, ENSG00000122971 ACADS, ENSG00000126457 PRMT1, ENSG00000144824 PHLDB2, ENSG00000140545 MFGE8, ENSG00000135521 LTV1, ENSG00000107771 CCSER2, ENSG00000147874 HAUS6, ENSG00000164733 CTSB, ENSG00000103671 TRIP4
#> ENSG00000136717 BIN1, ENSG00000273080 RP11-301O19.1, ENSG00000168701 TMEM208, ENSG00000108826 MRPL27, ENSG00000067955 CBFB, ENSG00000183647 ZNF530, ENSG00000117000 RLF, ENSG00000165983 PTER, ENSG00000104047 DTWD1, ENSG00000167232 ZNF91
#> Negative: ENSG00000153107 ANAPC1, ENSG00000153140 CETN3, ENSG00000181035 SLC25A42, ENSG00000164306 PRIMPOL, ENSG00000064651 SLC12A2, ENSG00000147536 GINS4, ENSG00000163577 EIF5A2, ENSG00000197568 HHLA3, ENSG00000197157 SND1, ENSG00000241839 PLEKHO2
#> ENSG00000156170 NDUFAF6, ENSG00000169499 PLEKHA2, ENSG00000224597 PTCHD3P1, ENSG00000153767 GTF2E1, ENSG00000187514 PTMA, ENSG00000136169 SETDB2, ENSG00000099330 OCEL1, ENSG00000215039 CD27-AS1, ENSG00000149311 ATM, ENSG00000273117 AC144652.1
#> ENSG00000198677 TTC37, ENSG00000140307 GTF2A2, ENSG00000130787 HIP1R, ENSG00000125995 ROMO1, ENSG00000148248 SURF4, ENSG00000223759 RP11-353N4.4, ENSG00000135365 PHF21A, ENSG00000158805 ZNF276, ENSG00000259230 CTD-2555C10.3, ENSG00000145414 NAF1
#> 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: 22343
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.5141
#> Number of communities: 2
#> Elapsed time: 0 seconds