knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
knitr::opts_chunk$set(echo = F, warning = F, message = F)

p007n

Data loading and qc

Velocyto counts are loaded

Data Filtering

## $cluster_res
## [1] 2
## 
## $sample_name
## [1] "p007n"
## 
## $loom_file
## [1] "_data/_patients/velocyto/p007n.loom"
## 
## $nFeature_lower
## [1] 500
## 
## $nFeature_upper
## [1] 5000
## 
## $nCount_lower
## [1] 1000
## 
## $nCount_upper
## [1] 50000
## 
## $nFrac_s_lower
## [1] 0.3
## 
## $nFrac_s_upper
## [1] 0.9
## 
## $nFrac_u_lower
## [1] 0.1
## 
## $nFrac_u_upper
## [1] 0.7
## 
## $nFrac_a_lower
## [1] 0
## 
## $nFrac_a_upper
## [1] 0.2
## 
## $pMT_lower
## [1] 0
## 
## $pMT_upper
## [1] 0.8
## 
## $pHB_lower
## [1] 0
## 
## $pHB_upper
## [1] 0.1
## 
## $rel_comp
## [1] 10

Before filtering

## An object of class Seurat 
## 100542 features across 3484 samples within 3 assays 
## Active assay: spliced (33514 features)
##  2 other assays present: unspliced, ambiguous

After filtering

## An object of class Seurat 
## 100542 features across 1208 samples within 3 assays 
## Active assay: spliced (33514 features)
##  2 other assays present: unspliced, ambiguous

Data normalisation

Cell cycle scoring

Data scaling and dimensionality reduction

Elbow plot

Cell cycle phase

Cell type identification

Louvain clusters

Cluster marker genes

rank 0 1 10 11 12 13 14 15 2 3 4 5 6 7 8 9
1 TNFRSF17 MZB1 CLCA4 CD3E MS4A1 A2M HPGDS CRYBA2 SOX4 SELENBP1 HES1 ITLN1 ADH1C MUC2 CA1 CDKN2B-AS1
2 SLAMF7 IGHA2 PTPRR TRBC1 VPREB3 ZNF385A BMX AC020661.2 HES1 CA2 SOX4 KLK1 UGT2B17 REP15 PIGR TMIGD1
3 DERL3 FKBP11 GUCA2B CD7 BANK1 CLEC7A COL27A1 FMOD TMSB10 CA1 HIST1H4C CLCA1 TXN CLCA1 CA2 C11orf86
4 MZB1 IGHA1 ABCG2 CD3D HLA-DQA1 SPARCL1 SH2D6 LY6G6C HEXIM1 KRT19 HEXIM1 MUC2 NXPE4 TFF3 CES2 CEACAM1
5 PRDX4 JSRP1 CA4 CD3G CXCR5 TGFBI PSTPIP2 CLCA2 RPL35 ADIRF ID4 SERPINA1 CD24 KLK1 SELENBP1 SLC51B
6 FKBP11 DERL3 GUCA2A IL2RB HLA-DPB1 CALD1 SH2D7 ANO1 RPS18 FABP1 ZFP36L2 REP15 UGT2A3 MLPH SLC26A2 GUCA2B
7 POU2AF1 SSR4 CEACAM6 TRAC LY86 AXL B4GALNT4 HAMP ID4 PHGR1 BX284668.6 WFDC2 NXPE1 FCGBP KRT19 CEACAM7
8 SEC11C XBP1 TRIM31 NKG7 LINC01781 CD36 TRPM5 MUC5AC RPS19 CKB MTRNR2L12 RNASE1 GPX2 RETNLB ADIRF AQP8
9 UBE2J1 JCHAIN C11orf86 CST7 ARHGAP24 SPARC CCDC129 PCAT18 NRARP PIGR HIST1H2BG TFF3 HMGCS2 ITLN1 CD24 HSD17B2
10 MANEA TENT5C MDK CD2 PAX5 CD93 PTGS1 KRT78 RPL31 KRT8 AL031777.3 SPINK4 PIGR ST6GALNAC1 FABP1 MS4A12
11 CD79A HSPA1B HKDC1 GZMA HLA-DRA SERPING1 HCK KLK15 IER3 CES2 KLLN FCGBP ATP5MC1 ANO7 KRT20 SULT1A2
12 TSC22D3 TGFB1 SECTM1 TRBC2 AFF3 PTGS2 IL17RB AL645940.1 HIST1H2AH FXYD3 PRR3 TPSG1 HBB SPINK1 PHGR1 GUCA2A
13 CD27 DPP7 CDA HOPX BLK LST1 OGDHL ASGR1 RPL36 CHCHD10 RMRP ST6GALNAC1 ATOH1 HMGCS2 SLC9A3
14 VIM JUN TMEM37 LCK FCMR MS4A6A LRMP CCDC149 RPL13 LGALS3 AC005837.1 REG4 SYTL2 BSG CA4
15 DUSP5 CD79A SELENOP CD247 LTB LAMA4 HTR3E TNFAIP8L3 SOCS1 LGALS4 HIST1H2AG MB RAP1GAP KRT8 HSD3B2
16 PIM2 LGALS1 SLC17A4 KLRB1 HLA-DRB1 COL4A1 ALOX5 SI HIST1H2AG ATP5F1D AL137077.2 SPDEF SERPINA1 GOLM1 SLC17A4
17 TENT5C HSPA1A AQP8 GPR65 CXCR4 IGSF6 AFAP1L2 SMIM33 RPL28 ATP5ME CSKMT SPINK1 DLL1 C10orf99 SLC26A3
18 JCHAIN HSP90B1 MUC12 FYN CCR7 VSIG4 FYB1 AZU1 TMEM238 BSG HIST1H2AH HEPACAM2 SYT7 CDHR5 PLAC8
19 PRDM1 VIM EMP1 CD160 RIPOR2 CCL2 AZGP1 PFKFB4 RPL13A S100A6 Z93241.1 MLPH MCF2L LGALS3 PRAP1
20 TRAM1 CCR10 CEACAM7 GZMB HLA-DPA1 STAB1 C12orf74 KIAA1324 RPS2 S100A14 AC103702.2 ANO7 MUC4 CKB CD177
21 SPCS2 NFKBIA MYO15B TRGC2 CD52 GNB4 HTR3C RAP1GAP MAFB LGALS2 MUC4 AGR2 ZG16 UQCRC1 TRPM6
22 MANF DUSP5 SDCBP2 GZMM LAPTM5 PLXND1 CHAT MFSD4A AC023157.3 TMEM54 AC012485.3 TMEM61 L1TD1 CHCHD10 LINC01133
23 SPAG4 IGKJ5 SLC9A3 SH2D2A HLA-DMB CLEC10A DCLK2 RAB15 ZFP36L2 CD24 AL391121.1 CDC42EP5 WFDC2 LGALS4 PRSS3
24 HERPUD1 NR4A1 PRAP1 HCST TNFRSF13C CXCL8 DPYSL3 JPH1 AL137077.2 C10orf99 AL136040.1 FOXA3 WNK4 DSP KRT20
25 AC104699.1 HSP90AA1 RHOF CCL5 HLA-DQB1 HTRA1 CD300LF PRKCG RASD1 ELOB AC007613.1 RAP1GAP CREB3L1 GPT C1QTNF12
26 ANKRD28 CD27 HSD17B2 IFNG CYBB THBD POU2F3 TPSG1 RPS15 SLC26A2 HIST1H4H ZG16 AGR2 S100A14 ANPEP
27 SSR3 CYBA CFDP1 FYB1 LY9 PTN ST18 NTN4 RPS9 PPDPF NRARP WNK4 SCNN1A ATP5F1D PHGR1
28 BST2 ICAM2 CDHR2 KLRD1 CD37 PMP22 IGSF3 AL133297.2 CSKMT ATP5MC3 IER3 CREB3L1 SPINK4 ELOB TMEM54
29 GNG7 BTG2 ENTPD8 ANXA1 GPR183 FSTL1 GRK5 CRACR2A IER5L PRSS3 LINC01970 RETNLB SLC4A7 TMEM54 ETNK1
30 MIR29B2CHG PIM2 TM4SF20 CD52 SLC2A3 C1QB KCNQ4 BEST2 RPS21 UQCRC1 HSPA2 BEST2 CBFA2T2 PPDPF FABP1
31 IGHA2 JUND SLC26A3 LCP1 RILPL2 AIF1 NRG2 AC005833.1 RPL37A UQCRQ AL355075.4 BCAS1 ERN2 MYH14 RHOC
32 LY96 HERPUD1 RFK CD8A CD83 MPEG1 KIT AC008397.2 RPL18A COX5B AL627171.1 SLC9A3R2 VMP1 S100A6 KRT19
33 RASGRP3 IGKC ANPEP GPR171 FCRLA CD209 PLCG2 SLC2A10 RPS29 ACADS MIR194-2HG ERN2 PRKAG2 FXYD3 KRT8
34 HSP90B1 SDF2L1 LMO7 LINC01871 CORO1A SDC2 CGNL1 DCBLD2 TXN BLOC1S1 CDKN1C LRRC26 INSR GPA33 PI3
35 EMP3 FKBP2 PLAC8 CD96 CCR6 CSF1R PLCB2 ARFGEF3 RPL8 KRT18 AC023157.3 DLL1 ENTPD8 ATP5MC3 PRDX6
36 CRELD2 SLAMF7 AQP7 PRF1 SWAP70 SMARCA1 MATK STXBP6 RPL12 ROMO1 AC091271.1 AC005833.1 TFF1 NDUFB7 FXYD3
37 JSRP1 AC104024.1 CD177 TMIGD2 TCF4 CPED1 TBC1D2B ARG2 OLFM4 CDHR5 HIST1H4E ERI3 MTRNR2L12 AHCYL2 LGALS3
38 SSR4 ANKRD28 SLC6A8 GATA3 RASSF2 BGN CCSER1 FOXA3 HIST1H3G NDUFB7 IER5L CRACR2B ATP2C2 SLC26A3 SDCBP2
39 TXNDC15 GLA CEACAM1 LCP2 CD53 COX7A1 PTPRJ C4orf47 CLDN4 TXN CLDN4 SCNN1A KLF4 PHLDA2 ACAA2
40 SPCS3 DNAJB1 FRMD1 CREM BAG2 RBPMS ADGRG6 MYRIP RPS16 UGT2B17 RHOB B3GNT6 TPM1 SULT1B1 DEFB1
41 PDIA6 UBC MEP1A CLEC2D LCP1 LILRB2 AVIL HRH1 MARCKSL1 COX6B1 ELF3 NPDC1 ELF3 HSD11B2 MISP
42 NUCB2 FCRL5 SLC15A1 CLEC2B LYN CPVL FRY HEPACAM2 HIST1H3A C19orf70 MARCKSL1 KRT18 GSN CHP2 C2orf88
43 SPATS2 ORAI2 MS4A12 DOK2 BCL2A1 GAS7 CORO2B FAM84B RPS8 CHP2 VEGFA CAPN9 GDF15 UGT2B17 PPP1R14D
44 HSPA5 AC093797.1 DST PTPRC BCL11A ENG HIP1R SLC25A44 RPL37 SLC39A5 SOX9 SCGB2A1 RASD1 KRT18 ADIRF
45 SELENOM ZFP36 TRPM6 EVL EBF1 GNG11 LIMCH1 CCNJL POLR2A C4orf48 ILF3-DT ATOH1 RASEF GGT6 SFN
46 ICAM2 PPP1R15A MIER3 KIR2DL4 LINC00513 COL5A1 ANXA13 ALDH1A1 RPL27A HMGCS2 AL118516.1 FAM3D TCIM SFN IFI27
47 IL10RA POU2AF1 EFNA1 SPOCK2 RGS19 TNS1 SPTLC2 AP001266.1 RPL29 HSD11B2 ARGLU1 RAB26 TMC5 CYC1 MUC12
48 SRGN RGS1 LAMB3 CD69 CD79A CLEC11A TREH GALNT8 PIGR PFKL MAFB ENTPD8 ANKRD36C ATP5ME TMEM120A
49 MEI1 IGLL5 SULT1A2 LAPTM5 SESN3 PLS3 CSMD1 RAB27A HIST1H4A KRT20 CEBPB GALNT5 MUC13 COX5B C3orf85
50 IRF4 UBB SMIM5 SAMSN1 TUBA1A C1QC PTPN18 TSPAN13 RPLP2 PADI2 TRIM8 SYTL2 DST TMSB10 CHMP2A
51 DNAJB1 RRBP1 GPRC5A SYTL3 IRF8 IL1R1 ADAMTS9 RETNLB RPS27 UQCR11 AL135925.1 GSN MVP DDAH2
52 EVI2B PDIA4 TNFSF10 ITGA1 CD74 PLAU ATP2A3 DCLRE1A ATP5ME GAPDH TPM1 COX6B1 TSPAN1
53 TIMP1 CCDC69 CNKSR3 TNFRSF9 GRASP COL14A1 SLCO3A1 COLCA2 HMGB1 SLC22A18 VSIG2 PLCE1 PKIB
54 HSPA13 GNG7 ABCB1 TNFRSF1B LINC00926 PREX2 GANC GNE MSX1 SULT1B1 TSTA3 MS4A12 SMIM22
55 RPN2 HSH2D APPL2 ARHGDIB PTPRC CMKLR1 ZFHX3 ELOVL7 MUC4 SMIM22 LGALS4 FAM213A HHLA2
56 GLA AL360012.1 RHOC ALOX5AP ZNF331 COL15A1 ARHGEF38 CAPN9 CLDN3 MS4A12 S100A6 MAPK3 CTSA
57 XBP1 ICAM1 LINC01559 GLIPR1 AC058791.1 EHD2 DKK3 ITLN1 RPL38 MISP SH3BGRL3 PAPSS2 PLS1
58 SEL1L SEC11C C1orf115 CORO1A POU2F2 HCAR2 ITPR2 DLL1 HIST1H4C COX6C RAB27A MISP S100A6
59 TXNDC11 ITGB7 CEACAM5 GNLY NFKBID FLT1 MGAM2 FRZB Z93241.1 DHRS11 NEURL1 CLDN3 PPDPF
60 C16orf54 RAB30 LRP4 TIGIT REL ISLR RASSF6 MB RPL18 AMN IGFBP2 ARL14 BLOC1S1
61 CYTIP HSPA1L SLC51B SLA PIP4K2A CCDC80 LUC7L3 FGF11 ATP5F1E ATP5PF FABP2 SULT1A1 SGK2
62 HSPA1B LINC00309 TMIGD1 IL7R GTF2B ITIH5 NEBL MEST NUPR1 MT1G IFI27 MOGAT3 S100A10
63 RAB30 IGKV3-20 SLC16A9 PTPN22 SNX2 SLIT3 CHD6 ANXA13 NOTCH1 TXNDC17 NANS COX6C ETHE1
64 HSPA1A TNFRSF17 SAMD9 RORA CREM CD86 TPM1 ZNRF3 RPS12 TMSB10 RPL36 EPCAM CLTB
65 CLPTM1L PRDM1 HPGD STAT4 CD48 CD4 CHDH KCNE3 YBX1 COX7B HPCAL1 FLNB SRI
66 DNAJC3 UBE2J1 EPS8L2 TRAT1 CYTIP CAVIN1 FGFR4 SCN8A ELOB S100A10 MCF2L AURKAIP1 PRR13
67 SRPRA IGKV4-1 LRRC1 TNFSF14 HLA-DMA CRIP2 MYO1B CYB5D1 ELF3 TJP3 MLLT3 ATP5F1E MYL6
68 LGALS1 TSC22D3 LYPD8 XCL2 HLA-DOB NCF2 KALRN SERPINA1 PPP1R15A ASL KLF4 TSPAN8 FLNB
69 DAPP1 DUSP2 SRI XCL1 NAP1L1 FCER1A DEPDC7 CMTM8 MKI67 TCEA3 ELF3 FUCA1 NAPRT
70 IGHA1 FAM30A ISG15 CTSW SAMSN1 CAVIN3 MAP7 CREB3L1 GSTP1 BICDL2 MYO5C NDUFV1 CDHR5
71 HSP90AA1 IGLV3-1 SPATS2L SLA2 MEF2C LMO2 IFI6 WFDC2 AC011498.1 UQCR10 RPL38 GAPDH OCIAD2
72 TPST2 SSR3 SLC22A5 BCL11B ARHGDIB COL6A2 GRASP FAM174B CYC1 AKR1C3 FRYL UQCRQ TST
73 FNDC3B HSP90AB1 TMPRSS2 CD6 GNB5 CLIC2 FES RNASE1 TIMM13 CISD3 COX6C OPLAH CA2
74 SDF2L1 GPBP1 PLIN3 SKAP1 CARD11 SDC3 SPIB CCDC196 HIST1H2BG PLCD3 RPS24 ANXA2 USH1C
75 LMAN1 HSPD1 LINC01133 RASAL3 SYPL1 TYROBP LIPG TACSTD2 NDUFB7 SUCLG1 L1TD1 C4orf48 C19orf33
76 IFNAR2 SEL1L PLOD2 SLC2A3 ARRDC2 IGFBP7 MTSS1 LUZP2 RPL19 AOC1 GDF15 PRSS3 PKP3
77 KLHL6 ANKRD36 CCDC68 TRDC SP110 C1QA ADH6 CATSPERG RPL32 TST URAD PLCD3 MPST
78 GYPC AC245014.3 CLDN23 ITK ADAM28 FPR3 FURIN AL035661.1 PRRG2 ETHE1 PLXDC2 ENDOG BSG
79 UBC PPP1R15B MISP RAB8B CD40 LIMS2 TAS1R3 DIXDC1 RPS24 LIMA1 TFF1 TRPM4 SLC9A3R1
80 HSPD1 HDLBP HHLA2 SLFN5 SP140 MS4A7 TET2 FA2H RPL10A TSPAN8 TCIM MRPL41 COL17A1
81 CCR10 HSPH1 IFI27 CD53 RUBCNL COL6A1 SPTLC3 RUNX1 COX5B GPT SMIM22 ALKBH7 JPT1
82 AMPD1 PDK1 CDHR5 ZNF331 BASP1 TNFSF13B LRRC75B CREB3L4 GPX2 PRDX5 GADD45G MALAT1 EFHD2
83 BASP1 AC020916.1 TSPAN1 FASLG APBB1IP DNASE1L3 TMEM63A SGMS2 HIST1H3H SFN RARRES1 NDUFS7 MYL12B
84 RGS1 PABPC4 NDRG1 RGL4 CHORDC1 IL1B NAV2 KRT4 RPL14 FAM213A PLCB4 ZBTB7A GIPC1
85 CHPF FBXW7 GBP3 ITM2A SMAP2 TSPAN4 MYO5B SMIM3 NAALADL2 CSTB SLC4A7 RHOB DHRS11
86 AL365361.1 HSPA8 ALDOB DUSP4 HLA-DOA C1orf54 GPR89A MLPH ABR ATP5MD RPS12 IER5L CHP1
87 HSPA6 ST6GALNAC4 PKIB TUBA1A RUNX3 FBLN1 ACTN1 DPYSL2 PLCB4 LGALS3BP CD63 AMN TMEM82
88 RGCC H1FX SCARB1 PDE4A SKIL RCAN2 SNX9 KCNMA1 RPL11 TRPM4 RPL27A TMEM238 HPGD
89 HSPH1 MIR29B2CHG CDKN2B-AS1 PRMT9 MIR29B2CHG COL4A5 PBXIP1 ATAT1 POU3F1 CLDN3 TCEA3 C19orf70 AMN
90 IGKJ5 RAPGEF1 GPA33 LAT IGHD NID1 INPP5B SCGB2A1 GAPDH PYCARD ARFIP2 ATP8B1 MYLK
91 PDIA4 IGLC2 MUC13 PREX1 NR4A2 PLAT MYO15B MBOAT2 HIST1H2BI MVP RASD1 PKM AOC1
92 SPCS1 SPCS3 MXI1 GZMH RNF139 LHFPL6 IL13RA1 KLK1 ATP5F1D ID1 DPM3 CYCS LYPD8
93 MIR155HG PDE4B SMPDL3A RBMS1 DRAM2 OLFML2A EIF1B PROX1 ATP5MC1 MGAT4B SLC12A2 AOC1 CSTB
94 THEMIS2 HYOU1 TCF7L2 RAC2 PRDM2 CD300E INPP5D B3GNT6 ATP5MC3 COX7A2 FAM83E TST SULT1A1
95 AQP3 FNDC3B CASP7 S100A4 LYSMD2 C5AR1 KMT2C GALNT12 AL118516.1 ATP1B1 AGR3 ATP5F1B MALL
96 PDE4B GYPC PLS1 COTL1 BCAS2 LMOD1 TLE4 STX1A PLCE1 BLVRB ID1 ETFB APPL2
97 KLF2 DNAJC1 PRSS3 SRGN KBTBD8 PCDH18 ALOX5AP REP15 RPS5 ATP5IF1 HES6 HADH IGSF9
98 HSP90AB1 KLF2 RETSAT RASGRP1 CD47 RBMS3 SOX9 REG4 IER5 SULT1A1 RPL37A SDC4 CKB
99 REEP5 FOS PTTG1IP NR4A3 DCK NNMT MEGF9 KDELR3 COX6C DSP S100A13 DSC2 TMPRSS2
100 HSPA8 FOSB HSD3B2 LRRN3 TBC1D9 PTX3 ERBB3 CAPN8 CHCHD10 GOLM1 S100P MYL6 TSPAN8

separation of epithelial, stromal and immune cells

Cell split