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

p008n

Data loading and qc

Velocyto counts are loaded

Data Filtering

## $cluster_res
## [1] 2
## 
## $sample_name
## [1] "p008n"
## 
## $loom_file
## [1] "_data/_patients/velocyto/p008n.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 2709 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 1307 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 2 3 4 5 6 7 8 9
1 CCR7 OLFM4 GNG13 FMOD IGFBP5 CEACAM7 HLA-DQA1 KLF5 CD8A REP15 MZB1 REP15 TNFRSF17 TRDC CEACAM7
2 IL7R PLCE1 BMX RAP1GAP SPARCL1 SLC26A3 MS4A1 PLA2G2A CCL5 WFDC2 DERL3 ITLN1 DERL3 HOPX GUCA2B
3 CTLA4 MTRNR2L12 SH2D6 NEURL1 BGN MS4A12 HLA-DOA LEFTY1 NKG7 ITLN1 IGLV3-1 MUC2 MZB1 KIR2DL4 GUCA2A
4 TRAC NAALADL2 TRPM5 TPPP3 NOTCH3 CEACAM1 LY86 IGFBP2 GZMA SPINK4 CD79A SERPINA1 CD79A TMIGD2 SLC51B
5 CXCR4 SELENBP1 HCK IL1R2 TNS1 GUCA2A ITGAM PIGR HOPX KLK1 IGKJ5 ST6GALNAC1 ADA2 KLRD1 SLC26A3
6 PASK LEFTY1 SH2D7 COL16A1 CSPG4 SLC51B LILRB2 CES2 CST7 MUC2 JCHAIN SPINK4 POU2AF1 TRGC2 CEACAM1
7 CD28 PLA2G2A HTR3E SERPINA1 SYNPO2 C11orf86 MS4A7 CD24 CCL4 SERPINA1 FKBP11 FCGBP SLAMF7 GZMA MS4A12
8 SPOCK2 PIGR HPGDS KLK1 CALD1 SLC9A3 HLA-DRB5 HMGCS2 GZMM REG4 CCR10 REG4 AC104699.1 PTPN22 PRAP1
9 FXYD5 LCN2 PSTPIP2 FOXA3 RERGL SULT1A2 MS4A6A AQP1 CD3G SPDEF GNG7 KLK1 MEI1 CD7 SULT1A2
10 GPR183 PLCB4 B4GALNT4 RETNLB COL6A2 GUCA2B STAB1 GPX2 CD3D TPSG1 SSR4 ATOH1 UBE2J1 CCL5 CA4
11 SELL ATP2C2 PTGS1 REP15 CCDC3 SDCBP2 KYNU SELENBP1 CD52 TFF3 TNFRSF17 WFDC2 EAF2 CD160 HSD17B2
12 MAL MIR194-2HG ALOX5 GNE RCAN2 CA1 MARCH1 C10orf99 TRAC FCGBP PIM2 TFF3 GNG7 NKG7 CA1
13 LTB GAS6 OGDHL REG4 LMOD1 ANPEP CD163 LCN2 CD3E CDC42EP5 IGHA2 SPDEF PIM2 CTSW SLC9A3
14 SRGN ABR LRMP CREB3L1 A2M SLC17A4 CLEC4E UGT2B17 HCST MUC4 XBP1 MLPH LY96 TNFRSF9 CDA
15 TSHZ2 CLDN15 COL27A1 BEST2 SUSD5 AQP8 LINC01857 OLFM4 CD2 ST6GALNAC1 FCRL5 MUC4 SPAG4 ITGA1 C11orf86
16 CD3E ZKSCAN1 KLK11 GALNT8 ANGPTL1 TRPM6 CD300E ADIRF LCK MLPH CD79B AGR2 FAM49A LDLRAD4 CEACAM6
17 LEF1 CES2 AVIL ANO1 SPARC HKDC1 TCL1A GOLM1 S100A4 RETNLB POU2AF1 BEST2 SEC11C SAMSN1 SDCBP2
18 TSC22D3 FERMT1 IL17RB CCNJL CAV2 CA4 OLR1 SLC39A5 IFNG ZG16 IGKV4-1 TPSG1 BASP1 GPR171 AQP8
19 ICOS MAVS PLCG2 WFDC2 EFHD1 C1QTNF12 FPR1 KRT19 PTPRC KRT18 SDF2L1 RETNLB RAB30 LAYN CA2
20 ZNF331 HMGCS2 DEFB1 SPDEF PLN HSD17B2 IGHD FABP1 CD69 AGR2 LGALS1 ANO7 SSR3 EVL SFN
21 CD4 GPX2 PAK3 ARFGEF3 CRYAB SLCO2A1 CXCL8 SOX4 ANXA1 IFI27 SLAMF7 GSN JCHAIN GPR65 MISP
22 PNRC1 KIFC2 CD300LF PER2 MYH11 CDHR5 VCAN ADH1C CTSW HSD11B2 SEC11C RAB26 IGHA2 GZMB COL17A1
23 PTPRC NOXO1 POU2F3 NEDD4L MGP CA2 S100A8 MT1G LCP1 CLDN3 SPAG4 ZG16 CRELD2 CD3E ANPEP
24 SLC2A3 HES1 IFI6 ATOH1 SLC7A2 MUC12 CPVL PRSS3 CD7 LRRC26 HSP90B1 FAM3D FKBP11 SYTL3 MUC12
25 BTG1 AC103702.2 AZGP1 ITLN1 NEXN CDHR2 MNDA ACADS XCL2 SPINK1 A1BG BCAS1 TMEM45A HCST DHRS9
26 EIF1 SOX9 TAS1R3 ST6GALNAC1 SNCG FABP1 LMO2 HES1 CD8B RNASE1 CD74 MCF2L MIR155HG CD3G HHLA2
27 SARAF NUPR1 HIP1R CAPN9 CPE SGK2 CSF1R PLCE1 CD48 ANO7 CD27 IL1R2 TXNDC15 MSN UGT2B17
28 PIK3IP1 KLF5 TMEM74B TMEM61 TIMP3 PDZD3 MPEG1 PCK1 TNF FAM3D HERPUD1 HSD11B2 LINC02384 CD3D RHOD
29 FYB1 NBEAL2 KIT DNAJC12 IGFBP7 DST AQP9 GAS6 TRBC1 SH3BGRL3 CYBA ERN2 PRDX4 FYN PDZD3
30 RPS13 LIMA1 ADGRG6 FRZB MAFB TM6SF2 VSIG4 KCNN4 KLRD1 S100P ZBP1 B3GNT6 CCR10 CD52 PRSS3
31 EEF1A1 CDH17 BATF3 MFSD4A LRRC10B MEP1A NCF2 MT1E RUNX3 KRT8 IGHA1 CRACR2B LGALS1 LINC01871 TMIGD1
32 DDX5 ABCC3 KLK13 TSPAN13 CAVIN1 EMP1 PAX5 TMEM238 KLRB1 NEURL1 JSRP1 CREB3L1 ICAM2 PDE4A MEP1A
33 CD3D SNHG19 DPYSL3 FHL2 MAP1B HHLA2 BANK1 LIMA1 ARHGDIB SLC9A3R2 SSR3 FABP2 CLPTM1L LCK SLC17A4
34 JUNB MLXIP DCLK2 GMDS ADIRF SFN FCER1G TSPAN8 LAPTM5 KLF4 ICAM2 NEURL1 SPCS2 CLEC2B FABP1
35 RPS27A PYCARD GRK5 KIAA1324 HES1 LINC01133 CLEC7A PPP1R1B CXCR4 MB EAF2 GALNT5 DUSP5 CST7 CDHR5
36 BCL11B MAFB RGS13 SPINK4 C11orf96 PDE9A HLA-DPB1 PLPP2 TNFAIP3 LGALS4 TENT5C ENTPD8 CD27 GLIPR1 CLCN2
37 TRBC1 ARL14 NRG2 MUC2 MYL9 MIR194-2HG CD22 NOXO1 TRBC2 ERN2 FKBP2 HEPACAM2 IGLV3-1 CREM SULT1A1
38 TIGIT BCAM AP002498.1 TOP2A HPGD HLA-DRA S100A16 ARL4C SMIM22 PDK1 RNASE1 IGLC7 ARHGDIB PDE9A
39 RPS4Y1 MATK LDLR CRIP2 IGSF9 ZNF385A CDX1 JAML ATOH1 IGKC SCNN1A PRDM1 SPRY1 AGPAT2
40 CD48 ANXA13 ETS2 CYR61 UGT2B17 SDS S100A14 STK17A TCIM LINC02362 SPINK1 U62317.5 DOK2 KRT20
41 HSPA8 AFAP1L2 HID1 KANK2 BTNL3 FCN1 MT1X PIP4K2A ELF3 AC104024.1 KIAA1324 FCGR2B NR4A3 TSPAN1
42 NR4A2 CCSER1 RNASE1 CDKN1C C3orf85 MIR3945HG CHP2 ALOX5AP ENTPD8 FAM30A CDC42EP5 HERPUD1 SLA2 DHRS11
43 GMFG ASCL2 HBEGF CSRP2 PLAC8 HCAR2 TKT DUSP2 BEST2 IGHGP SYTL2 HSPA13 PTPRC TM6SF2
44 MCUB PTPN18 TPSG1 WTIP CEACAM6 CLEC10A CA2 SRGN AC005833.1 SEC61B TFF1 TCF4 AC058791.1 MALL
45 TRBC2 JAG2 ESRP1 MKI67 TSPAN1 MS4A4A PYCARD TRGC2 CLDN4 DPP7 L1TD1 ANKRD28 NR3C1 GNG12
46 RPS27 GRASP RAB26 HMGB1 CRYBG2 FCRL1 TSPAN6 ID2 GSN BTG2 WNK4 RASGRP3 COTL1 ACAA2
47 FYN HTR3C GALNT5 MT1E C1orf115 AIF1 UQCRQ LINC02446 B3GNT6 ICAM1 SLC12A2 THEMIS2 TNIP3 PLAC8
48 TNFAIP8 CAMP LRRC26 HIST1H3G SLC6A8 CD93 CDH17 PARP8 CAMK2N1 ISG20 GMDS EDEM1 PIP4K2A TMEM82
49 FCMR RASSF6 UNC5B-AS1 SOX4 AC254629.1 EREG TUFM PTPN22 RAB26 UBE2J1 QSOX1 MEF2C HIC1 CHP2
50 LAPTM5 ZFHX3 ATF3 LINC01970 GPT RAB31 CEBPD CORO1A DNAJC12 EMP3 IFI27 FCRL5 SKAP1 CES2
51 RPL5 SLCO4A1-AS1 AGR2 RHOB CYP2B6 NPL AL137077.2 GZMK NPW OSBPL3 TSPAN13 TENT5C PRF1 TMEM54
52 CD37 FYB1 B3GNT6 C21orf58 HMCN2 HAS1 EMP2 COTL1 SNORC LINC00309 HID1 SSR4 ARHGAP9 FXYD3
53 RGCC PRSS22 SDR16C5 ACTA2 EFNA1 GAS7 MT1F GIMAP7 TSTA3 DNAAF1 SYT7 CHST2 FASLG GPT
54 RPS3A KCNQ4 OVOL1 AL355075.4 KRT20 LST1 PFKL GZMB RPL36 TRAM2 NEDD4L CTSH DUSP4 CDHR2
55 CD40LG NMU IL13RA1 YBX3 PRSS8 CD83 LGALS3 CD37 IER3 ADA2 CAMK2N1 LILRB1 ST3GAL1 PLCD3
56 YPEL5 SPIB PLXDC2 FXYD1 MOGAT3 HLA-DMB MLXIP GZMH ERI3 RAB30 MUC5B CD79B SIRPG PEPD
57 ARL4C ALOX5AP CCDC149 HIST1H3B TMEM37 HLA-DMA CISD3 H3F3B COX5B DUSP5 MTRNR2L12 IGKJ5 TNFRSF1B CDKN2B-AS1
58 DNAJA1 LUC7L3 RHPN2 RBPMS PRAP1 ADGRE2 MAFB MSN CREB3L1 IGHG1 HPCAL1 PNOC PGK1 AOC1
59 CD69 LYZ RAB15 NANOS1 MUC17 PTGS2 CD9 RAC2 RBBP8NL VIM ATP2C2 ELL2 SRGN GGT1
60 BCAS2 TRHDE MLPH SEPHS2 MYO15B TMEM170B TMSB10 TMSB4X SOX4 IGLC3 RRBP1 MANEA SCML4 C2orf88
61 CREM EIF1B DLL1 CEBPB CA12 HLA-DPA1 CLDN4 RASGRP1 VSIG2 IGHG3 S100P TRAM1 PARP8 PRSS8
62 NPM1 ANXA4 MTSS1L GSTP1 TMPRSS2 CYBB QPRT CD53 GMDS HSPA1B ACSS2 MANF AOAH BTNL8
63 RPL34 LIPG SCNN1A PLA2G2A FXYD3 S100A9 CLDN15 SLC2A3 PPDPF SEL1L NPW SLC1A4 CD247 TRPM6
64 RPL30 HOTAIRM1 FCGBP WDR34 AQP7 IRAK3 DSG2 HIC1 PHGR1 BASP1 PLCB4 SEC61B SH2D2A SLC6A8
65 RPL19 SPTLC2 RARRES1 TONSL AOC1 SIGLEC10 LGALS4 REL CLCA1 CRELD2 AGR3 XBP1 LINC00513 BTNL3
66 RPL9 TREH CRACR2A NFIB INPP5J VPREB3 MT1M THEMIS RASD1 MANF SLC9A3R2 IGLL5 ZNF331 PHGR1
67 ARHGDIB MAP7 FAM174B AP2S1 PLS1 ASGR1 NDUFV1 GNAI2 FABP2 IGHV3-48 LGALS4 SPCS3 CNOT6L FLNB
68 ITM2A CD14 MUC13 MFGE8 SHROOM1 SIRPA CYC1 APBB1IP BCAS1 EIF2AK4 GALNT7 CSF2RB CYTIP SRI
69 TUBA1A ITPR2 AKAP5 ITGA7 CES2 TYROBP FAM213A SAMSN1 IL1R2 PPIB MUC5AC SPCS1 TRBC2 LGALS3
70 H2AFZ CRIP1 LRRC31 MT1A PTK6 C3AR1 UQCRC1 ZNF331 HPCAL1 SPCS3 TSTA3 DAPP1 STK17A KRT19
71 ETS1 CHD6 SLC12A8 MT2A SRI SPI1 LGALS3BP RPS27A GDF15 GYPC RBBP8NL IGLC6 IL2RB TST
72 CD52 MARCKSL1 PRUNE2 ATAD5 FRMD1 LILRB3 MUC5B FYN PRDX5 ORAI2 SMIM22 HSP90B1 LIMS1 ASS1
73 KLRB1 KRT18 SLC12A2 IER5L LMO7 C5AR1 KCNQ1 RPS4Y1 EDF1 IGHV3-23 EMP2 VIM STOM MYH14
74 ZNF831 TPM1 IRF6 BCL7C MISP LYN SOX9 TPT1 NANS CCDC69 MICAL1 SLC7A7 LCP1 PKIB
75 RPS12 PPDPF TTC39A CLDN15 GPA33 HLA-DRB1 TIMM13 TUBA1A FAM83E PABPC4 ENTPD6 CD180 CD96 GPA33
76 SMAP2 MYO1B FAM13A GADD45GIP1 C2orf88 POU2F2 ECHS1 IL7R NDUFB7 RGS1 FAM83E IL10RA RARRES3 ACVRL1
77 TNFRSF4 PLEKHB1 RAB11FIP1 NUPR1 PHGR1 TNFRSF13C FAM3D AC058791.1 FOXA3 PRDX4 TPM1 CADM1 CCL4 HMCN2
78 CD2 TLE4 MB FGFR4 TMC5 CFP ELF3 NR4A2 COX6B1 DNAJC1 PTPRF IKBIP TMSB4X GPRC5A
79 LDHB TPM1-AS GSN IFITM3 GDPD3 GNB4 ATP8B1 MYL12A DLL1 MIR29B2CHG TPCN1 ISG20 CD69 USP2
80 RPS25 GDPD5 SLC39A11 HIST1H2AH GPRC5A CSTA TMEM54 GPR171 URAD PRDM1 EPCAM EMP3 PDCL3 CTSA
81 CCNI BIK TP53INP2 AL139274.2 MAL2 ADAP2 FCGRT CREM TM4SF5 SEL1L3 ELF3 PABPC4 ITGAE RHOC
82 RPL21 LY6H TCEAL9 NUCKS1 CLDN23 BCL2A1 ZKSCAN1 JUNB SCNN1A HDLBP ERI3 SRPRB PIK3R1 AKR1B10
83 RPL4 PBXIP1 SMIM14 IGFBP4 CLCN2 BTK EPCAM RORA COX6C HSH2D SLC44A4 SPATS2 LSP1 TRIM31
84 CD44 MTSS1 AGR3 GPRC5A TMEM45B HLA-DQB1 FERMT1 LCP2 RRBP1 TMEM258 CLDN3 B4GALT3 CORO1A MVP
85 CD6 THOC5 PPRC1 EMP2 USP2 LAPTM5 MGAT4B ETS1 TMSB10 CLPTM1L CLCA1 TRIB1 JAML GDPD3
86 SESN3 PRSS3 ARG2 TMEM238 DOK4 IGHM FABP5 LTB HSPB1 KDM5D LIPH BST2 STK17B S100A6
87 RPS28 CREG1 HSD11B2 CCDC124 ID1 BASP1 EPPK1 DDX5 BLVRB SPCS2 MYO6 A1BG ALOX5AP RHOF
88 LAT NRGN CKAP4 ATP5MC3 RHBDF1 RNASE6 MT2A DNAJA1 FER1L6 IGKV3-11 AMN ICAM1 PPP1R18 IFI27
89 RPS15A FGFR4 SEC23IP TPX2 PCK1 TNFSF13B IGFBP4 HSPA8 S100A6 SPATS2 CLDN4 SDF2L1 CMTM3 EFNA1
90 RPL11 MIR200CHG EMP2 TK1 FLNB SLC7A7 COX4I1 XCL1 L1TD1 TXNDC11 TCIM SEL1L TNFAIP3 HPGD
91 RPSA TM4SF5 KLF4 ENAH NEAT1 SNN ATP5MC1 IL2RB NDUFA1 TP53INP1 NUPR1 CD38 TUBA1A EMP1
92 RPS7 ASRGL1 MUC4 SFN CTSA RCSD1 COX5B RPS12 PTMS HSPA1A AL390719.2 ALG5 IKZF2 PCK1
93 NACA ATP2A3 ERI3 OAT DQX1 FES LPP TAGAP BLOC1S1 SELENOS CD63 FNDC3A RGS1 PTPRR
94 H3F3B TPD52L1 KRT12 RPL35 TSC22D1 C1orf162 PRSS8 RARRES3 KRT20 SRM MGLL LINC02362 CD53 FUCA1
95 CD3G H2AFJ SCG5 MT1X AKR1B10 LYL1 LTBR CD99 RPS15 IGKV3-20 PCCA PDIA6 SERPINB9 SLC26A2
96 CD247 FURIN EGR2 LAMB2 EPS8L2 PHACTR1 CLDN3 UBE2S NPDC1 KLF2 NANS CXorf21 APBB1IP PRR15
97 RPL10 TMC5 MBOAT2 AC023157.3 TMEM120A CXCL2 ST14 FYB1 MT1G SPCS1 FAM162A NCF1 DOCK8 LMO7
98 BTF3 IL13RA1 RASEF KCTD12 PIP5K1B SLC8A1 IMPDH2 RPSA GALNT8 FNDC3A MUC13 SERP1 RAC2 ETHE1
99 RPS6 ACADSB ANO7 ASPM TRIM31 PLEK TRAP1 SARAF HID1 POU2F2 PDIA3 BTK ISG15 FBLIM1
100 RPS20 GSTP1 DLGAP4 ETFB TCF7L2 LAT2 BSG RPLP1 CHCHD10 ERLEC1 ITGB7 TRBC1 MGLL

separation of epithelial, stromal and immune cells

Cell split