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

p009ot0

Data loading and qc

Velocyto counts are loaded

Data Filtering

## $cluster_res
## [1] 2
## 
## $sample_name
## [1] "p009ot0"
## 
## $loom_file
## [1] "_data/_patients/velocyto/p009ot0.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 17313 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 15147 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 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 28 29 3 30 4 5 6 7 8 9
1 PI3 LCN2 RPLP2 LGALS1 FABP1 NEAT1 RPLP2 LYZ LYZ LCN2 TUBA1B BHLHE40 NDUFA4L2 NOTUM NDUFA4L2 FABP1 REN BHLHE40 TFPI2 CCL20 LCN15 REG3A HSPD1 REG3A CDCA7 CLSPN
2 S100A11 LYZ RPL6 VIM LCN15 MALAT1 RPL6 LCN2 LCN2 HMGB1 PTTG1 EIF1 NDRG1 RPL23 FABP1 DHRS9 SLC26A3 DUSP5 IGFBP5 CXCL1 LDHA CA6 RAN NOTUM PCNA PCNA
3 ANXA1 RPS14 RPS2 MT2A CKB KCNQ1OT1 RPL27A CLDN2 SNORC TUBA1B HMGB1 SAT1 CKB RPL19 CKB REN CEACAM7 REN PLAT CXCL3 LINC00239 LCN2 HMGB1 PRSS56 GINS2 TUBA1B
4 IL18 RPL23 RPL27A TPM2 PCCA RPS2 HSP90AA1 CLDN2 PTTG1 H2AFZ GAPDH LDHA RPS23 LCN15 LGALS3 DHRS9 FXYD3 STC1 PI3 RPL27A NOTUM TUBA1B CA6 MCM4 FAM111B
5 S100A10 RNASE1 RPS13 PLAT TFF3 RPS13 HMGB1 COL11A2 EIF4EBP1 PTMA VEGFA LCN15 COMMD6 TFF3 FXYD3 FXYD3 NDUFA4L2 IGFBP7 SLC26A3 CDX2 LYZ HMGB2 WNT6 HSPD1 HIST1H1B
6 ANXA2 COL9A3 RPS12 IGFBP7 PHGR1 NACA TUBA1B RNASE1 CAPS CCNB1 MALAT1 TFF3 RPS14 FXYD3 PHGR1 EMP1 MALAT1 TPM2 CXCL2 TFF3 CCND2 H2AFZ APCDD1 MCM6 GINS2
7 UCA1 ID1 CDCA7 TIMP1 LGALS3 RPLP0 HSPD1 AGR2 PSMA7 NPM1 ENO2 ANKRD37 S100A4 LDHA PCCA CEACAM1 INSIG1 MMP3 LINC00520 RPS13 CLU PTGES3 PROX1 NCL H2AFZ
8 KRT18 CAPS PEBP1 PLAU GPA33 FAM3D RAN CD63 PTMA DTYMK CLIC3 P4HA1 RPL12 NDRG1 CSTB PKIB S100P SPON2 TM4SF1 ENO1 CLDN2 HSP90AA1 DKK4 HIST1H4C HIST1H4C
9 KRT8 CXCL14 NACA IGFBP5 LDHA PEBP1 TESC COL9A3 NDUFS6 TUBB4B RPL37 PGK1 RPL37 LGALS4 CKB CEACAM5 S100A14 MMP1 KRT20 FAM162A NEAT1 NCL DPEP1 MCM3 HMGB1
10 PERP ASCL2 COL6A2 PRDX5 TSPAN8 SNORC SSR4 HSP90AA1 NCL INSIG1 VEGFA RPS18 PGK1 LINC01559 LINC01559 VEGFA VIM EMP1 IFI27 HSPE1 NKD1 HIST1H1B BRCA2
11 MSX2 PTGES3 COL6A1 CDX2 ASCL2 TALDO1 PIGR ATP5MC1 HNRNPAB RPL28 C4orf3 C9orf16 KRT19 LGALS4 FABP1 CSTB PTGS2 NFKBIA APCDD1 SNRPF SP5 BRCA2 CDC6
12 CCND1 RAN CAV1 HSPD1 MLEC NEAT1 MRPL51 RANBP1 ZFAS1 INSIG1 PERP LGALS3 TSPAN1 TSPAN1 SDCBP2 C11orf96 CEACAM6 PCSK1N PTMA GPR155 HELLS MCM3
13 ANXA3 HSPD1 TAGLN PLCB4 HSPE1 TSPAN8 HMMR HSPD1 S100P FXYD3 RPL23A MIR210HG EMP1 SDCBP2 NEAT1 PLAU CEACAM7 NBDY CBX5 TDO2 H2AFZ MCM6
14 VSNL1 ATP5MC3 GNG11 NAP1L1 RRM1 TESC CENPF SNRPB HES4 RPS18 RPL21 PCK1 CEACAM6 PSCA S100A6 GNG11 S100A11 RNASE1 BIRC5 FGF20 RAN HNRNPAB
15 SLC2A1 PLCB4 FN1 RPS26 HMGB2 TALDO1 COL9A3 CYCS RPL32 FAM162A CXCL14 FAM162A LCN15 CEACAM6 CEACAM6 SELENOM S100P NKD1 SET AC036222.1 TUBA1B ATAD2
16 SLC7A11 SNRPF CALD1 PTGES3 CENPF SELENBP1 CCNB1 MRPL51 RPS27 RPL12 RPL28 EGLN3 PKIB PHGR1 SAT1 FGF7 TRIM31 SSR4 LDHB PTK7 MCM7 HELLS
17 MRPL51 NAP1L1 MT1E COX5A TOP2A MAGED2 CCT5 NDUFS6 PDLIM4 SCD TPT1 C4orf3 CD24 PTPRR ERO1A FN1 KLK10 MGAT5 RANBP1 KRTAP3-1 HMGB1 TUBB
18 NDUFS6 LDHB PITX1 EIF3F PTGES3 ID1 TUBB4B PCNA NDUFA4L2 KRT19 GABPB1-AS1 PHGR1 PRDX5 KRT20 EIF1 FGL2 IER3 GALNT6 ATP5MC3 CCND2 GMNN PTMA
19 KRT23 RPS26 THY1 GMDS TMEM106C CDK6 TOP2A CCT5 RPS19 GAPDH CST3 PIGZ TFF3 DUOX2 FTH1 COL1A2 GGH SPINK1 PEBP1 SLC1A5 RRM1 GMNN
20 ATOX1 FAM3D SPARC TESC FAM3D CXCL14 CYC1 HMMR RPL12 EIF4A2 PHGR1 TPI1 AKR1C3 LYPD3 CLIC3 TMEM158 PHGR1 BIK ECT2 MAP1B CDC6 NCL
21 ACTN4 TSPAN8 COL1A1 AGR2 PRDX4 WFDC2 TFDP1 SNRPG ANKRD37 PLOD2 RPL38 LINC01559 KRT20 CD24 UBC SPARC SLPI DPEP1 RRM1 DACH1 UNG DTYMK
22 DTYMK HMGB1 EMP3 EIF4EBP1 HDAC2 CKS2 BIRC5 RPS18 MIR210HG EPB41L4A-AS1 PCCA SQOR TRIM31 ELF3 NRG1 UCA1 SH3BGRL CKS2 ASPSCR1 PTGES3 MCM4
23 PTTG1 ATP5MC1 CTGF TUBB4B LDHB RPL31 DDIT3 IL18 FAM13A C10orf99 CSTB EPCAM IL11 IL18 TSPAN8 HSP90AB1 SOX4 CDT1 HIST2H2AC
24 CCT5 NCL MYL9 ETS2 HSPE1 EFNA1 RPL32 KRT23 C10orf99 ETHE1 LGALS4 EFNA1 SFRP1 ANXA2 ASCL2 CDCA7 ITPR2 SNRPF TUBB4B
25 MET COX5A TUBA1A RANBP1 PRELID1 S100A14 FAM13A TPD52L1 GPA33 S100A14 DUOXA2 TM4SF1 BST2 CSTB GRN CCT2 SLC7A8 CLSPN NASP
26 PCCA EIF5A STC1 NUCKS1 TUBB EIF4A2 RPL13 RPS25 PTPRR GPA33 LGALS3 KRT20 CTSK CXCL8 ABHD2 CDK4 KRT23 EIF4EBP1 UBE2T
27 SFN HSPE1 CYR61 CCT2 SLC25A5 GADD45B RPLP2 IFI27 CD24 DBI CKB CCL20 TPBG ADIRF SLC40A1 HNRNPD ASCL2 POLR3K MCM7
28 TUBB4B LSM5 SELENOM UBE2C SET KRT19 RPL27A KRT8 CDX2 CEACAM1 S100P UPK2 COL6A2 CLDN4 SLC7A8 MAD2L1 MDK NOP56 HSPD1
29 HNRNPAB GMDS CCDC68 EIF4G2 CENPF RPS16 CLIC3 PCSK1N P4HA1 PRR15 ADIRF HES4 COL3A1 AREG IFI6 MKI67 CENPX BRI3BP LMNB1
30 CCNB1 LSM7 CLEC2B SMC1A TFDP1 RPS14 RPS19 SLC2A1 KRT20 S100P DSC2 EMP1 CXCL5 S100A14 ALDH2 TMPO HES6 HIST1H1E TYMS
31 HSPA8 CYB5A CAVIN3 AGR2 PSMA7 NDRG1 TXNIP MUC13 ACOT13 TPI1 GPRC5A ARRDC3 TFPI PCCA SELENBP1 TPX2 PCSK1N ORC6 ATAD5
32 S100A16 ETS2 NNMT MKI67 HMGB3 RPL10 EFNA1 RNASE1 INSIG1 LIMA1 SCEL GAPDH THY1 KRT8 S100A4 TUBB4B SYK CCT2 RANBP1
33 YBX3 COL3A1 CKS2 SUB1 TXNIP ERO1A C6orf48 LINC00239 SRI CCL20 CD24 CLEC2B SDC4 TNFSF15 CENPF TSPAN5 PTMA NPM1
34 GGH SPON2 DKC1 ODC1 RPL36 LRP1 TGFBI SCD UCA1 S100A14 KRT19 HSD17B2 DSC2 ISG20 DEK MAN1A1 SRSF7 DUT
35 EZR CARD16 ASCL2 MKI67 RPS15 RPL31 FDFT1 GPX2 S100A6 CD55 ADAMTS1 GPRC5A HLA-A HIST1H4C AREG PEBP1 GMPS
36 JPT1 DKK3 HIST1H4C EI24 ACTG1 NACA AGR2 KRT18 SRI SH3BGRL3 COL1A1 TST AREG YBX1 CD46 DCTPP1 TK1
37 HMMR CCL2 CAPS RPA3 RPL11 RPS8 ETHE1 TMPRSS4 GGH ANKRD37 CLMP KRT18 PIGR SNRPD1 RCN1 RANBP1 HIST1H1E
38 CKS2 COL1A2 NHP2 TMSB10 TPT1 PPARG SLC25A5 HK2 NDRG1 COL12A1 SERPINB1 FTL NOP56 CLU HSPE1 CENPK
39 KPNA2 CTSK NASP RPS21 EIF1 SLC22A18 CDH17 TMEM45B TFF3 F2R FXYD3 CST3 EIF4EBP1 SESN3 FAM111B DCTPP1
40 EDIL3 SRSF7 RPL35A RPL11 LIMA1 GGH CLDN4 TMBIM1 PXDN RHOC RCN1 BRCA2 GJB1 CDK4 HIST1H1C
41 MAP1B TOP2A SCD RPL13A RBCK1 GPRC5A NDUFA4L2 SERPINB1 BMP2 SQOR ATP1B1 RPS26 KCNQ1OT1 HIST1H1C SNRPB
42 LYPD1 GTF3A DDIT4 RPL28 ENO1 KRT8 ELF3 PHGR1 COL6A3 SQSTM1 ATRX MLEC WASHC3 LDHB MKI67
43 COL12A1 TPX2 S100A6 RPL10 ARHGAP18 NFE2L3 SH3BGRL3 CLDN3 PDGFRA LGALS3 PRR13 HMGB3 LASP1 SLBP CENPX
44 C11orf96 CCT7 RPL24 RBCK1 MARCKS CHCHD10 CLIC3 LGALS4 BDNF SFN SNORC FABP5 MGAT5 DEK TFDP1
45 PRRX2 EIF5A RPL37A PDLIM4 TXNIP PHLDA2 TFF3 SCD FGF2 REN CD63 SNRPA1 MAP2K6 USP1 CCT5
46 TMEM158 MRPL22 RPL34 LGALS4 VEGFA CAST HHLA2 S100A10 SLC16A6 KRT6B CD46 SRSF7 COX20 MAD2L1 RFC4
47 COL6A3 PHB2 EPB41L4A-AS1 RPS13 SHMT2 CDX2 NEAT1 GPRC5A MRC2 SRI PSAP PHGDH AL031058.1 PRKDC DNMT1
48 NR2F1 KPNA2 RPS23 MSMO1 ACSL3 FABP5 BHLHE40 ATF3 A2M PHLDA2 TRIM44 ODC1 REG1A RPLP2 PPM1G
49 F3 UBE2C RPL7A RPL29 GPRC5A SERPINB1 RPL37 EDIL3 IFI27 CXCL14 NUCKS1 ACAA2 ATAD2 RFC2
50 COL4A2 HIST1H4C RPS24 RPS24 SRI TM4SF1 GADD45B TRPA1 NEU1 SMC1A ABHD2 MSH6 USP1
51 COL18A1 CKS2 ELF3 ZNF292 KCNQ1OT1 RNF186 LAMB3 FSTL1 SOX4 POLR3K CERS6 SET MAGOHB
52 CCDC102B SLC2A1 DDIT4 WSB1 EGLN3 ADIRF RGS2 TMSB4X HIST1H1B PAM XRCC2 TOMM40
53 MCAM FTH1 RPL35A CDH17 KRT80 CEACAM7 IGFBP6 ARMCX3 PLCB4 SFN HSP90AB1 PTTG1
54 A2M CCNI NEAT1 INSIG1 C4orf3 RAB34 CD24 PRKDC CCND1 ATP5MC3 SRSF7
55 CAVIN1 HMGCS1 PCCA PCCA SDC4 GJA1 EIF4G2 PSMA4 SUPT4H1 RFC4 SET
56 PXDN CSTB RPL10A TMBIM1 EIF4A2 HGF SYAP1 CKAP5 HLA-A ODC1 HSP90AB1
57 EVA1B RPS8 RPL34 PPP1R14D ACTG1 FOXF1 SRSF3 CHPF SRPK1 TOP2A
58 COL4A1 RPS11 ITM2C ETHE1 TSPAN1 RPS4Y1 FAM3D GRN CENPU SLBP
59 AKAP12 UBC MALAT1 KRT19 CKB MMP2 MTCH2 TSC22D1 ATAD5 WDR34
60 FSTL1 SNHG8 S100A14 CD9 TMEM45B VCAM1 ANP32B PHLDA1 YBX1 CCT6A
61 PTN DDIT3 ELF3 CPEB4 HMGCS1 TUSC3 DYNLL1 TGFBI NASP SIVA1
62 TFPI RACK1 PPDPF SRPX2 TXNIP ADAMTS5 PTTG1 GGH DNMT1 H2AFX
63 SFRP1 S100A10 AGR2 C4orf3 RPL28 LOXL2 BRI3BP SNORC HSP90AA1 SRSF2
64 RAB34 RPL5 ZFAS1 MUC12 CEACAM1 DSEL NAP1L4 KRT18 HACD3 TUBA4A
65 MSN RPL29 JUND ACSS2 CIB1 WNT5A COX5A S100A4 TUBB RPA3
66 HTRA1 RPL13A KDM3A UBC LINC00520 PTGES CNBP DUT LDHB
67 FOXF1 PPDPF S100P TACSTD2 FHL2 FAM20C DKC1 LYAR BIRC5
68 ENG RPL10A CCNI ARL14 TRIM31 SPOCK1 TUBB TMPO SMC1A
69 ITGA1 SLC20A1 HERPUD1 KLK10 UBE2B IL13RA2 TALDO1 SRSF2 DDX46
70 NES RPL18A PRSS8 EDN1 CCNI SNCA ATP5F1B ALYREF RAD51AP1
71 IL1R1 RPS5 NEU1 PPARD GSN BNIP3 EIF5A PHGDH PRELID1
72 CD248 RPS3A KCNQ1OT1 VEGFA JUND LOX FUS CBX5 XRCC5
73 RPS4Y1 P4HA2 BTG1 TMPRSS4 P4HA2 SLC6A15 ALYREF SNRNP25 CENPH
74 ITGA8 ANXA2 WSB1 ATP1B1 MSMO1 EFEMP1 WDR43 FANCI PSMA7
75 THBS1 CD9 CLDN3 CAST CAST TCF21 SRPK1 SMC1A PAICS
76 COL5A2 P4HA1 DSP CLDN3 PERP PDLIM3 PHLDA1 FAM3D HSPE1
77 PDGFRA LAMB3 LINC00239 FTH1 ACSL3 CHST2 ANAPC5 HMGB2 MAD2L1
78 HSD17B2 ACSL3 LGALS3 CD55 PPDPF SFRP2 TOP2A C1QBP ODC1
79 SERPINE1 OSER1 KRT20 EFHD2 LGALS3 NOVA1 CCT6A HNRNPD ALYREF
80 NEXN JUND ENO1 MALAT1 ZFAS1 GPR68 MRPS34 MRPS34 CDCA7
81 FHL1 RBCK1 LMAN1 FHL2 OPTN COLEC10 C1QBP CCT6A SUPT16H
82 AXL PPP1R15A FDFT1 RBP2 RHOC PAMR1 PSMC3 CENPV RRM1
83 ANTXR1 LDHA ACSL3 UCA1 EZR TCEAL7 PSMD13 MTHFD2 SNRPG
84 LHFPL6 RPL14 ZKSCAN1 PI3 LDHA THBS1 TCP1 SNRPA1 MSH6
85 TSPAN4 C4orf3 KLF5 SCD SPRR3 CTHRC1 HACD3 NAE1 HSPA8
86 ABCC4 CAMLG GPRC5A RHOC KLK10 FKBP10 C11orf58 NAP1L4 EBNA1BP2
87 FGF7 MSMO1 GALNT3 NDRG1 TMEM59 FBN1 UBE2N NUDC FABP5
88 F2R EEF1A1 SLC6A8 LIMA1 PKIB COL8A1 RSL1D1 SRM MRPL51
89 ADAMTS1 CAST TPI1 TXNIP PDLIM4 MEDAG HNRNPA3 ANP32B DKC1
90 WFDC1 CLDN3 ATF4 EPCAM PGK1 IL6 SNRPG RFC2 SNRNP25
91 MYLK PIM3 GOLGB1 IER3 ACSS2 FENDRR IPO5 UBE2T ACAT2
92 MAP1A PGK1 GAN GSN CD9 COX7A1 HNRNPU RIF1 SMC4
93 EHD2 C6orf48 QPRT IFI27 DSC2 CCL2 TMEM106C PSAT1 HNRNPA2B1
94 ECM1 NEU1 PRSS3 DUSP1 SRI NR4A2 TFDP1 TFDP1 CYCS
95 TPBG GSN GFPT1 CAPG SCNN1A NDN GSPT1 CYCS HNRNPD
96 TCF4 UBE2B ABLIM1 SEMA5A ANXA2 CD248 SNRPB UBE2N PSMD12
97 BDNF GUK1 CDH17 AOC1 S100A11 SPART ARL6IP4 PPM1G NOP56
98 FAM20C VDAC1 HMGCS1 SORL1 CLDN4 GYPC ASCL2 SNRPD1 HSPA4
99 RAB3B RPL22L1 EPB41L4A-AS1 FDFT1 TMSB4X EMP3 MRPS26 FABP5 DEK
100 TRPA1 KRT17 GPA33 S100A10 P4HA1 EVA1B SFPQ CYB5A SRSF3
NA no_sig_genes no_sig_genes no_sig_genes no_sig_genes

separation of epithelial, stromal and immune cells

Cell split