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

p013ot3

Data loading and qc

Velocyto counts are loaded

Data Filtering

## $cluster_res
## [1] 2
## 
## $sample_name
## [1] "p013ot3"
## 
## $loom_file
## [1] "_data/_patients/velocyto/p013ot3.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 27511 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 24972 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 21 22 23 24 25 26 3 4 5 6 7 8 9
1 HIST1H4C S100A6 FABP1 CCL20 CCL20 HIST1H4C NCL CCL20 MALAT1 FABP1 HIST1H1C FABP1 ALDH1A1 RPS27A SLC26A3 ALDH1A1
2 CLSPN KRT19 SLC26A3 CXCL3 HIST1H4C DPEP1 HSPD1 CXCL3 NEAT1 SLC26A3 HIST1H2BJ DPEP1 RPS12 FXYD3 DPEP1
3 DEK NEAT1 LGALS3 CXCL3 ALDH1A1 HNRNPA2B1 CXCL2 MS4A12 HIST1H4H RPL21 RPS4X CEACAM6 CYP2W1
4 HIST1H1D MALAT1 LGALS4 CXCL2 HMGB1 HSP90AB1 MALAT1 DHRS9 HIST1H2BC HMGB1 RPL34 NEAT1 RPS27
5 BRCA2 S100A11 PHGR1 CXCL1 HIST1H1B DEK NEAT1 LGALS3 HIST1H2AC NCL RPL11 PHGR1 OLFM4
6 PCNA KRT8 MALAT1 HIST1H1B AKR1C2 EIF5B NFKBIA LGALS4 HIST3H2A AKR1C2 HIST1H4C CDH17 RPLP1
7 HSPD1 KRT18 FXYD3 HIST1H1D H2AFZ HNRNPU HES1 CEACAM6 SNRPD1 SERBP1 RPS15A ADIRF TNNC1
8 NCL TGFBI NEAT1 HIST2H2AC RPL21 NPM1 ELF3 KRT20 GTF3A RPL8 MALAT1 TPT1
9 HMGB1 TXNIP S100A6 NFKBIA BMP7 HSP90AA1 IER3 PHGR1 ANP32B RPL7A LGALS3 RPL12
10 GMNN S100A10 KRT20 TUBB AKR1B10 RIF1 MUC13 FXYD3 AKR1B10 FTL SLC40A1 RPL21
11 MCM3 KRT20 FTL UBE2C BRCA2 CENPF SELENBP1 S100A6 NUCKS1 RPS23 S100A6 PRDX5
12 TUBA1B ANXA2 S100P IER3 UBE2C TOP1 FTL AKR1C3 COX7A2 S100P RPL23
13 DNMT1 IFI27 S100A14 GDF15 RFC3 ZC3H13 AKR1B10 CNBP RPL10 TSPAN8 KRT8
14 MKI67 TM4SF1 CDH17 TUBA1B ID1 EIF3A CEACAM1 ZC3H13 RPS5 LGALS4 RPL27A
15 HNRNPA2B1 CCND1 CD24 UBE2T GSTP1 NUCKS1 S100P KCNQ1OT1 RPL18 KRT20 LCN2
16 SMC4 HLA-A SELENBP1 H2AFZ TFDP1 PRRC2C NEAT1 GPX2 SELENBP1 KRT19
17 TOP2A NEU1 KRT8 AREG RANBP1 SFPQ S100A14 HINT1 KRT8 KCNQ1OT1
18 DUT PERP ADIRF TOP2A TOP2A BDP1 KRT8 S100A6 CTSA CLDN2
19 AGR2 AGR2 HMGB2 ANP32B ATRX S100A9 UBE2C IFI27 GPX2
20 CD24 AKR1B10 BTG3 TUBA1B MKI67 AGR2 ATP5MC3 FTL RPSA
21 TIMP1 CES2 EREG UBE2T TPR S100A16 ATP5MC1 SLPI QPRT
22 TSPAN8 IFI27 GTF3A GOLGB1 S100A10 POMP NXPE4 PHGR1
23 ATP6V0E1 KRT19 HMGB2 CCT6A PLS1 UQCRH TMEM59 SELENBP1
24 MUC13 NCL ROCK2 SLC22A18 BRK1 FTH1 ZFAS1
25 SAT1 CNBP PRPF40A CDH17 MRPS6 TXNIP FTH1
26 HES1 AKR1C3 SYNCRIP ETHE1 SPCS1 HLA-A KRT18
27 IER3 ID3 ANP32B IFI27 LGALS4 TIMP3 CCND1
28 PPIG TSPAN1 H2AFZ TMEM45B ID1
29 HNRNPM CES2 ATP5PO ASS1 AKR1B10
30 HSPH1 ADIRF LSM2 C10orf99 HES1
31 RAD21 TSPAN8 SEC61G CAMK2N1
32 THOC2 MALAT1 SELENOW PPDPF
33 SH3BGRL3 DGAT1
34 TFF1 GRN
35 UQCRQ HLA-C
36 TMEM45B TMPRSS4
37 ASS1 LIMA1
38 KRT19 CES2
39 LIMA1 S100A14
40 KRT18 S100A10
41 DGAT1 NEU1
42 IL18 SLC22A18
43 SMIM22 HLA-E
44 MGST3 CD24
45 PHLDA2 ATP1B1
46 UQCR11 C9orf16
47 ATP1B1 AKR1B10
48 CD24 UQCR11
49 SAT1 RTN4
50 SELENBP1 GUK1
51 CKB LCN2
52 SH3BGRL3
53 SMIM22
54 PLS1
55 SAT1
56 KRT18
57 MUC13
58 GGH
NA no_sig_genes no_sig_genes no_sig_genes no_sig_genes no_sig_genes no_sig_genes no_sig_genes no_sig_genes no_sig_genes no_sig_genes no_sig_genes

separation of epithelial, stromal and immune cells

Cell split