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

p013ot0

Data loading and qc

Velocyto counts are loaded

Data Filtering

## $cluster_res
## [1] 2
## 
## $sample_name
## [1] "p013ot0"
## 
## $loom_file
## [1] "_data/_patients/velocyto/p013ot0.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 7562 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 6344 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 16 17 18 19 2 20 3 4 5 6 7 8 9
1 HIST1H1B TYMS SLC26A3 FABP1 PTTG1 AKR1B10 CCL20 SELENBP1 TUBB PRDX5 SLC26A3 MALAT1 ASCL2 NDRG1 TIMP2 PRDX5 NDRG1 TPT1 RPS19 RPS12 FABP1
2 CDK1 MYBL2 MS4A12 CKB TUBA1B EPHX1 CXCL1 PHGR1 UBE2C PHGR1 FABP2 NEAT1 HSP90AB1 ANKRD37 S100A11 HLA-A FAM13A PPDPF RPL13A RPL28 CKB
3 UBE2C GINS2 LGALS3 UBE2C HMGB1 ME1 MIR3142HG KRT8 GINS2 SELENBP1 AKR1B10 SLC26A3 IDH2 MIR210HG TM4SF1 DPEP1 MIR210HG CEBPB RPL18A RPS19 FXYD3
4 HIST1H4C UBE2T FABP1 HIST1H4C CCNB2 S100P NFKBIA C10orf99 H2AFZ CD24 TM4SF20 KCNQ1OT1 LYZ VEGFA CEACAM6 TSPAN8 CKB RPS27 NPM1 RPLP1 LDHA
5 TUBB ZWINT FXYD3 MYBL2 CCNB1 TXN CXCL3 CD24 TUBA1B OLFM4 PPDPF MUC13 CLDN2 LDHA SNCG TXNIP SLC6A8 C6orf48 VSNL1 RPS28 TDP2
6 HIST1H1D TUBB KRT20 HIST1H1B NPM1 FTH1 CXCL2 PRDX5 DNMT1 KRT20 AKR1C3 EFNA1 SELENOP KRT8 FABP1 EIF1 ITGA6 RPL12 SCD
7 MYBL2 PCNA CEACAM7 ANLN CDC20 FTL LCN2 CES2 MKI67 SDCBP2 DKC1 NUPR1 KRT20 FCGRT FXYD3 ZFAS1 PRMT1 RPL8 CSTB
8 BRCA2 UBE2C DHRS9 TYMS NCL PPDPF NFKBIZ HLA-A HIST1H4C CEACAM7 ALDH1A1 ZFAS1 RHOC HLA-C EGLN3 FTH1 NCL RPL32 MIR210HG
9 DIAPH3 FAM111B LGALS4 TOP2A HSPD1 AKR1C1 AREG HLA-C UBE2T CBR1 KCNQ1OT1 ZNF292 PHLDA3 ZFP36L2 TFF3 RPS12 EEF2 RPL36 PKM
10 DNMT1 BRCA2 ADIRF TK1 CENPF PRDX1 IER3 SLC26A3 RANBP1 EPHX1 PTTG1 CCL28 SQSTM1 EPCAM LGALS3 RPL13 HNRNPM RPS5 LGALS4
11 TOP2A H2AFZ FTL HIST2H2AC RANBP1 TALDO1 EREG CBR1 PPM1G HLA-A SLC6A8 EMP1 HLA-E ANKRD37 CCNI FBL RPS8 GPA33
12 MKI67 DEK SDCBP2 LDHA PTMA LCN2 SELENBP1 CTSA BRCA2 SELENBP1 PRR15L NEAT1 SOX4 LDHA S100P MYC RPL29 PHGR1
13 UBE2T TK1 IFI27 HIST1H1D H2AFZ CTSA PCK1 CDK1 FTH1 FAM13A PERP QPRT ZG16 SEPHS2 AREG RPL18 TPI1
14 TYMS CDK1 SLC51B TUBA1B RAN TSPAN8 PYCARD MCM7 FTL DSP SLPI KIAA1324 PIGZ RPS15A ETS2 RPL35A BNIP3
15 HIST2H2AC CLSPN SELENBP1 MKI67 HSP90AB1 C9orf16 GRN FABP5 S100P TFF3 ANXA2 BTG2 TDP2 MALAT1 RPS23 S100A6
16 CLSPN TUBA1B NXPE4 TPX2 HSPE1 CBR1 HLA-E TPX2 CTSA EIF1 PRSS22 CLDN3 KRT19 LCN2 RPS21 ENO1
17 FANCI MCM3 PHGR1 TUBB SRSF7 SLC22A18 DPEP1 DUT HLA-C TXNIP FTH1 KCNQ1OT1 C4orf3 C9orf16 RPL34 PGK1
18 PCNA CENPU CDH17 PKM TOMM40 AKR1C3 CHP2 HMGB2 MALAT1 PPP1R3G SAT1 CD24 TFF1 GPR160 TMSB10 C4orf3
19 TUBA1B RANBP1 MGLL CDK1 HNRNPM GSTP1 MAOA TOP2A AKR1C1 GPR160 ISG20 AP003774.4 LGALS4 CAMK2N1 FTL KRT19
20 MCM3 TOP2A S100A14 ZWINT TUBB4B KRT20 ITM2C CDCA7 C9orf16 C4orf3 HSPB1 TMEM59 CA9 DDIT3 RPL18A ACOT13
21 GINS2 FBXO5 C10orf99 FAM111B GINS2 PLA2G16 KRT18 UBE2S NEU1 CLDN3 S100A10 GRN PLAC8 MGAT4B RPS15 FDFT1
22 FBXO5 HMGB2 HSPB3 PTMA SRSF3 MGST3 FUCA1 SNRNP25 CASP5 DDIT4 TMBIM1 ASCL2 SORL1 EPHX1 RPL14 PTTG1
23 H2AFZ HELLS SH3BGRL3 HMGB2 ILF2 GUK1 CRYL1 TUBB4B MGAT4B EGLN3 TFF2 PPP1R1B SPAG4 HERPUD1 RPL10
24 HMGB1 MKI67 CEACAM6 UBE2T ANP32B CES1 TM4SF20 CENPK CDHR5 BTG1 FOXQ1 KRT18 PGK1 FTL RPL30
25 HELLS RRM1 KRT8 CLSPN DDX39A TM4SF20 LGALS4 SIVA1 SLC22A18 SPAG4 SERPINE2 UBB VEGFA HLA-A RPLP0
26 KIF23 ORC6 S100A10 FXYD3 NASP MGAT4B FXYD3 E2F1 SLC40A1 PNRC1 MAP1LC3B CES2 GAPDH EDF1 HMGA1
27 ZWINT MCM7 AKR1B10 BRCA2 DKC1 DGAT1 RNF186 CENPF HLA-E GCC2 S100P DSP PLOD2 SPINK1 CCDC85B
28 TPX2 RMI2 NEAT1 PCNA DTYMK KRT8 TMEM59 PLK1 TMEM59 KLF5 TUBB2A ALDH1A1 GPA33 LGALS2 SELENOW
29 CDC45 TPX2 IQGAP2 TPI1 PRMT1 NQO1 CD63 TFDP1 LCN2 C6orf48 PMEPA1 SLC12A2 C15orf48 PHGDH C19orf53
30 TK1 SNRNP25 PPDPF CENPK FABP5 FBXO2 GPR160 CKS2 EPCAM KRT19 ATP6V1G1 GPR160 EFNA1 MAOA TMEM238
31 ATAD2 MAD2L1 SLC22A18 CENPM TUBB PYGB CTSZ AURKA TALDO1 PLAC8 SDCBP2 CAMK2N1 PHGR1 NEU1 PPP1R14B
32 AURKB DTYMK S100P RRM1 SNRPB SEPHS2 LAMP1 CDH17 IRF2BP2 COL6A1 MALAT1 DUOX2 PSAT1 ZFAS1
33 MCM4 DUT MVP DNMT1 CSE1L DCXR ELF3 MGST3 ADD3 S100A14 ETS2 NEAT1 MDK EIF4EBP1
34 MND1 E2F1 AHCYL2 HJURP BIRC5 CYB5A IFI27 PRDX1 KLHL24 SH3BGRL3 PNRC1 SCD CTSA BOLA3
35 MCM7 CENPM CHMP2A MCM4 SNRPF SQSTM1 SMIM24 ITM2C SLC3A1 EIF1 CTSA RNF186 LAMP1 HIST1H4C
36 ASF1B IDH2 MYL12B MCM7 DLGAP5 CCNI ITM2B ADIRF PLOD2 KRT23 ITM2B CD24 TPP1 CTBP1
37 BIRC5 DSN1 CDHR5 GAPDH HMMR GSTA1 QPRT KRT8 CLDN4 MYL9 IGBP1 CSTB ITM2C DHCR24
38 RRM1 RAD51AP1 VDAC1 CDT1 CCT7 AKR1C2 FAM3D SNCG FHL2 CHPF C6orf48 PCK1 PYGB SLC25A39
39 CDT1 CENPX PTK6 FBXO5 LDHB PPIC DHRS11 SLC39A4 GDF15 PHLDA2 PKDCC MPZL2 TMEM219 SRM
40 HMGB2 CDT1 CES2 GMNN DNMT1 TMEM219 CARD16 HSPB1 DARS CDA ELF3 LAMA1 ASNS RPL41
41 RANBP1 HMGB1 ETHE1 FANCI CCT5 CEBPB CDH17 SELENOM BNIP3 SAA1 CD9 NXPE4 MYO10 NDUFAF8
42 MELK MCM6 S100A6 ASF1B SFPQ SERPINE2 MALAT1 ME1 ANKZF1 FBXO2 LYZ PKM H1F0 LSM2
43 CCNA2 RFC4 LIMA1 ENO1 MCM7 FIS1 CLDN3 MAOA PIGZ CD55 CCND2 CEACAM7 TMC5 TAGLN2
44 ANLN GMNN PRR15 H2AFZ HNRNPA2B1 GCLM AKR1C3 GUK1 GAPDH RHOD MAOA BHLHE40 EPB41L4A-AS1 CDCA7
45 SMC4 CENPK CEACAM1 ATAD2 HNRNPU SELENOM C15orf48 ITM2B TMEM59 HEBP2 GOLGB1 P4HA1 SARS SPG21
46 HIST1H1E CARHSP1 TMPRSS4 TDP2 XRCC5 ALDH1A1 AP003774.4 CHPF GFPT1 TGM2 LGALS2 ELF3 LRRC75A
47 GMNN RFC2 SLC25A5 CDKN2D CCT8 FAM210B AKR1B10 CES2 SNX9 S100A16 SH3BGRL CYP2S1
48 HJURP ASF1B UQCRQ SCD HNRNPAB AZGP1 SRI GRN C6orf222 ANXA3 TMEM176B NEDD9
49 NASP BRCA1 SAT1 GINS2 GMNN PSAT1 ALDH1A1 CAMK2N1 CEBPB LAMC2 ATP6AP2 TPI1
50 MAD2L1 NASP FTH1 FABP5 ENO1 PTGR1 TXNIP SLC46A3 KRCC1 PDGFA ZKSCAN1 PRR15L
51 FAM111B EMP2 PCK1 CCNA2 ODC1 C6orf48 ID1 LGALS3 ELF3 PI3 TSPAN3 SAT1
52 CENPK RPA3 OAF MCM3 SNRPD1 SLC7A11 KLF5 GPR160 PGK1 GPRC5A G0S2 TXNIP
53 NCAPG MCM4 CRYL1 C21orf58 PPM1G TSPAN8 LAMP1 TSC22D1 TNFRSF12A SLC44A4 P4HA2
54 DTYMK PGP TSPAN1 LIG1 LYAR IDH3G TSPAN13 ANKRD12 TIMP1 ATRX FOS
55 CENPM HAT1 RTN4 MIR210HG SYNCRIP LGALS2 HLA-B KDM3A SELENOM SRI MOGAT2
56 H2AFX MND1 S100A9 BIRC5 SET AKR1C2 C10orf99 ACOT13 GUK1 ZBTB38 SDCBP2
57 UBE2S HIST1H1B MGST3 NCAPG CENPW BTG2 MYL12A P4HA1 NEU1 OLFM4 BNIP3
58 DSCC1 FANCI DGAT1 MAD2L1 MCM3 LIMA1 PTGR1 CAMK2N1 UCA1 TNFSF10 ERO1A
59 DUT CENPH HSD11B2 HELLS NUCKS1 TST RTN4 ZKSCAN1 ADIRF RARRES1 KRCC1
60 FABP5 SRSF7 SULT2B1 CDC6 UBE2S PPIC LIMA1 DBP OPTN TMEM176A PLIN2
61 MCM6 FAM111A MYL9 NUSAP1 NOP56 MGST3 HSD11B2 HERPUD1 CXCL16 GAS6 KRT20
62 WDR34 ATAD5 CTSZ UBE2S PRPF40A HSD11B2 SEPHS2 ACTG1 LURAP1L PDZK1IP1 ANKRD9
63 TUBB4B SLBP FABP2 BTG3 MSH6 SLC44A4 ATP6V0D1 LGI4 ISG15 SPINK1 AC104534.1
64 RECQL4 HIST1H4C VAMP8 WDR34 CDCA7 SEPHS2 HPGD VAV3 PLA2G16 CLDN15 CES2
65 PTMA ATAD2 CD24 DBI CCT3 MVP CRYL1 NEDD9 S100A6 EPB41L4A-AS1 MXI1
66 SKA3 SMC1A CHCHD10 TUBB4B CDKN3 ZFP36L2 AKR1C3 CBX4 DDIT3 PDCD4 LGALS1
67 CENPF WDR34 CBR1 SMC4 TPX2 SELENOM DGAT1 MXI1 IFI27 EID1 PPARG
68 E2F8 BARD1 SMIM14 HMGB1 SNRPG FOS DST CREBRF GSN ECI2 ACSL3
69 NUSAP1 CTNNAL1 RHOC AURKB HSPA4 FCGRT FKBP2 UBC TMEM45B AL117382.1 CLDN3
70 LIG1 RBL1 CDKN1A DUT HNRNPA3 HLA-F CCNI ST14 SFN SYF2 S100A14
71 PRKDC CCNE2 SLC44A4 GPA33 SERBP1 TOB1 CHP2 TAF1D CDKN1C ADM
72 KIF11 PSIP1 PLCD3 RANBP1 CCT6A TNFSF10 CA12 CYP2S1 CEACAM1 PDK1
73 NCAPH DIAPH3 HEPH CTNNAL1 NOP58 LCN2 TSPAN8 HIST1H2AC YPEL3 S100A10
74 CENPU NUSAP1 TM4SF20 DTYMK LMNB1 IFI27L2 ATP1B1 EPB41L4A-AS1 CCND1 ACOT13
75 LDHB TMEM106C EPCAM CENPU HSP90AA1 SERPINB6 TMEM54 FXYD3 AL365226.2 LRP1
76 FAM83D CCNA2 GFER MND1 PSMG1 SH3BGRL EIF1 CAST FTL TSC22D1
77 PDCD5 KIF23 SQOR H2AFX CCT2 PDZK1IP1 TMEM45B PTTG1IP C9orf16 IFI27
78 KIFC1 CDC6 TMEM54 FDPS LBR ATP6V0D1 IDH3G STAU1 MYL12B IQGAP2
79 NCL E2F8 CMAS TAGLN2 DEK HLA-B TINAG SYBU CDHR2 AL133453.1
80 CDC6 DSCC1 S100A16 BRCA1 ADRM1 OSGIN1 TGOLN2 EPCAM BEX2 TNFSF10
81 RAN EZH2 ITM2C DIAPH3 PSMB1 TRAPPC6A TMEM8A HLA-E CDKN1A SLC44A4
82 TEX30 SIVA1 SGK2 SMIM3 MAD2L1 SLC39A4 MEP1A MALAT1 LAMB3 S100A6
83 ATAD5 PTMA DHRS11 ORC6 EIF4G1 HSPB1 ITPKA G0S2 DPP4 PTTG1IP
84 ORC6 ASRGL1 PLS1 NDRG1 SLBP HPGD SLC51B EIF4A2 IL18 CAST
85 CSE1L BTG3 PARM1 LMNB1 GPATCH4 FBP1 IQGAP2 IGBP1 SLC3A2 PTK6
86 DDX39A CLDN2 PTGR1 CKAP2 GADD45GIP1 HES1 SQSTM1 ADM DST C6orf223
87 PPM1G TUBB4B ATP6V0E1 TEX30 CCT4 ID3 TLCD2 WAC GDPD3 DDIT4
88 SPC25 PRIM1 TMEM59 TFF3 HNRNPDL AL365226.2 H1FX LIPH TMCC1
89 CHAF1B CENPW BLVRB TFF1 EIF5A DCXR YPEL3 DYNLRB1 MIF
90 DEK TEX30 SMIM22 C6orf223 PDCD5 SERPINE2 PLIN2 RRAS PLCB4
91 CHEK1 SMC2 ARHGAP18 DEK FBL SLC44A4 UBE2B CSTB ST14
92 RFC4 PRKDC CAST HNRNPAB SRPK1 OPTN ERO1A CPE QSOX1
93 KIF20B SPC25 ANXA2 EZH2 SSRP1 FBXO2 METRNL TNNC1 SLC2A1
94 SHCBP1 CHEK1 CAPG CSTB NOL7 VAMP8 LIMA1 SERINC2 FAM162A
95 GMPS CSE1L CA12 MCM6 SNRNP25 COX7A2 CCDC28A JUP ZFP36
96 TOMM40 XRCC2 SLC6A8 CENPW PAICS CHCHD10 ENO1 AREG CEACAM1
97 HNRNPAB SHMT1 CEACAM5 RFC4 TAGLN2 CD63 PLSCR4 BCL2L1 PDE8A
98 SRSF3 NCAPH FAM162A ACAT2 ALYREF CES1 BCL10 CLDN4 ADIPOR2
99 CTNNAL1 EXOSC8 ALKBH7 S100A6 TRIM28 TMEM219 FOSL2 PLCD3 KLF4
100 NDC80 RAN ANKRD9 PRKDC HNRNPH3 ABCB1 TDP2 PINK1 MYH14

separation of epithelial, stromal and immune cells

Cell split