ReferenceAnn_DE

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Last updated: 2021-07-05

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Knit directory: Embryoid_Body_Pilot_Workflowr/analysis/

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absolute	relative
/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/mergedObjects/Harmony.Batchindividual.rds	../output/mergedObjects/Harmony.Batchindividual.rds
/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/MostCommonAnnotation.FiveNearestRefCells.csv	../output/MostCommonAnnotation.FiveNearestRefCells.csv
/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Supp_RefAnnDE_cardiomyocyte.png	../output/figs/Supp_RefAnnDE_cardiomyocyte.png
/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Supp_RefAnnDE_hepatoblast.png	../output/figs/Supp_RefAnnDE_hepatoblast.png
/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Supp_RefAnnDE_mesothelial.png	../output/figs/Supp_RefAnnDE_mesothelial.png

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There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.

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library(Seurat)
library(limma)
library(edgeR)
library(Matrix)
library(dplyr)

Attaching package: 'dplyr'

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library(scater)

Loading required package: SingleCellExperiment

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Loading required package: GenomicRanges

Loading required package: stats4

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Loading required package: parallel

Attaching package: 'BiocGenerics'

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    clusterExport, clusterMap, parApply, parCapply, parLapply,
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merged<- readRDS("/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/mergedObjects/Harmony.Batchindividual.rds")

#load annotations
ann<- read.csv("/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/MostCommonAnnotation.FiveNearestRefCells.csv")

merged@meta.data$RefAnn<- ann$Annotation

DimPlot(merged, group.by= "RefAnn")+NoLegend()

clusts<- (unique(merged@meta.data$RefAnn))

#theres 1 thymocyte and it doesnt want to plot it. so removing
clusts<- clusts[-57]

#or myeloid
clusts<- clusts[-58]

#or excitatory neurons
clusts<- clusts[-66]

#or antigen presenting
clusts<- clusts[-65]

plts<- NULL
for (i in 1:length(clusts)){
  b<- clusts[i]
  plts[[i]]<- DimPlot(merged, cells= c(rownames(merged@meta.data[merged@meta.data$RefAnn == as.character(b),])))+NoLegend()+ggtitle(paste0(b))
}

plts

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#Add Group Metadata
Group<- factor(paste(merged@meta.data$RefAnn, merged@meta.data$Batch, merged@meta.data$individual, sep="."))

merged<- AddMetaData(merged, Group, col.name = "Group")

subset to: cells from groups that have at least 10 cells total

Ngroup<- table(merged@meta.data$Group)
Ngroup.keep<- Ngroup[Ngroup>=10]

merged<- subset(merged, subset= Group %in% names(Ngroup.keep))

submerged<- as.SingleCellExperiment(merged, assay="RNA")

sumex<- sumCountsAcrossCells(submerged, ids=submerged@colData$Group)

sumex<- sumex[,colSums(sumex)>0]

Group<- colnames(sumex)
cluster<- as.vector(substr(Group, 1, regexpr("*.B", Group)-1))
batch<- substr(Group, regexpr("Batch", Group),regexpr("Batch", Group)+5)
ind<-  substr(Group, regexpr("NA", Group),regexpr("NA", Group)+6)

samps<- cbind(cluster,batch,ind,Group)

dge<- DGEList(sumex, samples=samps, remove.zeros = T)

Removing 1809 rows with all zero counts

remove uncertain

dge<-dge[,dge$samples$cluster != "uncertain"]

keep cell types that have at least 4 groups (at least 2 individuals, at least 2 replicates)

ct.keep<- table(dge$samples$cluster)
ct.keep<- names(ct.keep[ct.keep>=4])

dge<- dge[,dge$samples$cluster %in% ct.keep]

23 cell types left after this cell/celltype filtering

#filtering genes

genes.keep<- filterByExpr(dge, group= Group)

dge<- dge[genes.keep,,keep.lib.sizes=F]

dge<- calcNormFactors(dge, method="TMM")

dge$samples$cluster<- as.factor(as.character(dge$samples$cluster))

#not including batch and individual in model because I do not have balances representation across cell types

design<- model.matrix(~0+ dge$samples$cluster)

v<- voom(dge, design, plot=T)

fit<- lmFit(v,design)

nclust<- length(unique(dge$samples$cluster))
contrasts<- NULL
for (i in 1:nclust){
    c<- c(rep(-1,nclust))
    c[i]<- nclust-1
    
    contrasts<- cbind(contrasts, c)
}

contrasts

       c  c  c  c  c  c  c  c  c  c  c  c  c  c  c  c  c  c  c  c  c  c  c
 [1,] 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
 [2,] -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
 [3,] -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
 [4,] -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
 [5,] -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
 [6,] -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
 [7,] -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
 [8,] -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
 [9,] -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
[10,] -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
[11,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
[12,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
[13,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
[14,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1 -1
[15,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1 -1
[16,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1 -1
[17,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1 -1
[18,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1 -1
[19,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1 -1
[20,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1 -1
[21,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1 -1
[22,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22 -1
[23,] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 22

fit<- contrasts.fit(fit, contrasts=contrasts)

efit<- eBayes(fit)

plotSA(efit)

summary(decideTests(efit))

           c     c     c     c     c     c     c     c     c     c     c     c
Down     271  1438   658   620   559  1067  1723  3322   479  1891   920   183
NotSig 11839  9768 11061 10995 11140 10216  9226  6595 11280  8806 10485 11993
Up       971  1875  1362  1466  1382  1798  2132  3164  1322  2384  1676   905
           c     c     c     c     c     c     c     c     c     c     c
Down     376  1190    91   643  2549   979   792   364   144   560  5167
NotSig 11533  9989 12383 11051  7843 10224 10696 11574 12148 11091  3273
Up      1172  1902   607  1387  2689  1878  1593  1143   789  1430  4641

levels(dge$samples$cluster)

 [1] "Amacrine cells"               "Cardiomyocytes"              
 [3] "Ciliated epithelial cells"    "Ductal cells"                
 [5] "Epicardial fat cells"         "Goblet cells"                
 [7] "Granule neurons"              "Hepatoblasts"                
 [9] "IG"                           "Intestinal epithelial cells" 
[11] "Islet endocrine cells"        "MUC13_D"                     
[13] "Mesangial cells"              "Mesothelial cells"           
[15] "Metanephric cells"            "Retinal pigment cells"       
[17] "SLC24A4_PEX5L positive cells" "Squamous epithelial cells"   
[19] "Stellate cells"               "Stromal cells"               
[21] "Thymic epithelial cells"      "Visceral neurons"            
[23] "scHCL.hESC"                  

For example, lets see the top genes DE by Cardiomyocytes (coef 2)

topTable(efit, coef=2, sort.by="P", n=50)

             logFC    AveExpr        t      P.Value    adj.P.Val        B
MYL7     130.66430  3.0976950 30.21845 1.847703e-54 2.416980e-50 46.30499
BMP4     100.17794  4.6916506 26.04480 2.482904e-48 1.244905e-44 47.33820
MYL4     128.60340  3.2151048 26.00579 2.855068e-48 1.244905e-44 43.38726
CYB5D1    83.34643  3.8300429 25.22105 4.896782e-47 1.601370e-43 38.70436
APOBEC3G  90.85741  2.0962458 23.72382 1.325661e-44 3.240680e-41 27.97143
DOK4      71.25664  4.8213956 23.69388 1.486437e-44 3.240680e-41 41.78124
CFC1     100.08962  1.1041893 22.03796 9.765033e-42 1.824806e-38 23.39502
HS3ST3A1  86.60612  2.1116755 21.92962 1.509262e-41 2.467832e-38 26.51592
GLIPR2    73.08017  3.9350171 21.68732 4.016454e-41 5.837692e-38 35.41663
BAG3      58.11844  4.2447476 21.03112 5.891112e-40 7.706163e-37 33.46104
FGF19    107.72012  2.2553657 20.82809 1.366447e-39 1.624954e-36 29.36165
BMPER     96.84503  2.3372969 20.16516 2.207314e-38 2.406156e-35 28.62389
TNNT2     92.88780  2.9350416 20.11749 2.701837e-38 2.718672e-35 30.65986
COBLL1    66.26504  3.8078148 18.55705 2.360551e-35 2.205597e-32 28.89878
DNAH2     87.33649  1.5861408 18.34031 6.195401e-35 5.402803e-32 20.95438
KRT19     65.97059  8.6797897 18.26668 8.610261e-35 7.039426e-32 49.52404
PLPPR5    84.77348  1.3670778 18.18679 1.231576e-34 9.476617e-32 18.83396
TMOD1     83.64226  1.9293714 18.15105 1.445832e-34 1.050718e-31 21.66704
PSKH2    102.71186  0.5888992 18.12316 1.638795e-34 1.078437e-31 18.74104
APLNR    121.89089  2.3444355 18.12179 1.648860e-34 1.078437e-31 29.79227
TMEM185A  53.09470  3.9425363 18.02878 2.505759e-34 1.506125e-31 27.13528
TNNI1    121.51287  3.9575031 18.02637 2.533044e-34 1.506125e-31 35.69392
RGS13    144.64986  2.6808708 17.99972 2.856335e-34 1.568971e-31 32.12976
HTRA1     80.66431  3.5987240 17.99800 2.878626e-34 1.568971e-31 29.75697
PRDM6     81.90209  1.8387960 17.78189 7.650104e-34 4.002840e-31 20.50841
LHFPL2    51.42098  3.8578678 17.43567 3.707501e-33 1.865301e-30 25.51257
ALPK2     86.60294  2.0494678 17.39412 4.485349e-33 2.173068e-30 22.24025
HAND1    134.92284  4.6368572 17.30063 6.890111e-33 3.218912e-30 37.49295
LYN       58.36667  3.5424557 17.05154 2.174038e-32 9.806410e-30 24.28785
SVEP1     71.29496  2.2052858 16.82727 6.159146e-32 2.685593e-29 19.22263
BAMBI     74.02825  6.5277939 16.79757 7.073195e-32 2.984660e-29 39.16688
SLC9A3R1  45.81782  6.6814823 16.76133 8.375453e-32 3.423728e-29 36.82614
HAS2      87.30497  5.5998335 16.66846 1.292503e-31 5.102493e-29 36.31877
ACTC1    112.70701  5.6095105 16.66295 1.326235e-31 5.102493e-29 40.55194
FABP5     58.77926  7.8679014 16.54164 2.341450e-31 8.751003e-29 44.09118
S100A11   45.05607 10.0171268 16.52148 2.573913e-31 9.352597e-29 48.96027
SHISAL2B  73.73926  2.6002339 16.10512 1.838141e-30 6.498575e-28 20.38247
TCF21     85.51477  1.8131395 15.90283 4.814762e-30 1.657419e-27 18.99167
FAM89A    76.32724  5.8430913 15.81296 7.397133e-30 2.481074e-27 36.12206
GYPB     109.95160  0.4211041 15.66734 1.486511e-29 4.861262e-27 16.12666
PPFIBP1   40.37845  5.1133169 15.50954 3.175936e-29 1.013279e-26 27.98998
TUBB6     57.58937  5.2111883 15.47312 3.785710e-29 1.179069e-26 29.67380
ADAM19    68.91500  3.7111987 15.43315 4.591396e-29 1.396745e-26 24.78315
ADGRA2    71.74334  2.0801881 15.35020 6.856677e-29 2.036366e-26 17.12242
HAPLN1   135.31468  5.1626583 15.34577 7.005309e-29 2.036366e-26 35.92405
MIXL1    109.03120  2.2806485 15.11656 2.131129e-28 6.060284e-26 22.94231
P3H2      58.24763  3.7355420 14.89919 6.156338e-28 1.713427e-25 22.47444
RGS5      89.58711  5.7892420 14.89128 6.399314e-28 1.743946e-25 33.65425
KDR       86.16713  2.9812211 14.69530 1.673609e-27 4.467853e-25 22.30438
HOXB6    110.90093  2.6245312 14.68790 1.735630e-27 4.540755e-25 24.16276

We see recognizeable markers of CMs in that list-- MYL7, MYL4, TNNT2

vol<- topTable(efit, coef=2, n=nrow(fit))
labsig<- vol[rownames(vol) %in% c("MYL7", "MYL4", "TNNT2"),]
labsiggenes<- rownames(labsig)
thresh<- vol$adj.P.Val < 0.05
vol<-cbind(vol, thresh)
v<- ggplot(vol, aes(x=logFC, y= -log10(adj.P.Val))) +
  geom_point(aes(colour=thresh), show.legend = FALSE) +
  scale_colour_manual(values = c("TRUE" = "red", "FALSE" = "black")) +
  geom_text(data=labsig, aes(label=labsiggenes))

v

png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Supp_RefAnnDE_cardiomyocyte.png", width= 6, height=6, units= "in", res= 1080)

v

dev.off()

make list of top 20 most significant DE genes in each of the 23 cell types in this analysis

Top20DE<- NULL

for (i in 1:nclust){
  Top20DE[[i]]<- topTable(efit, coef=i, sort.by="P", n=50)
}

names(Top20DE)<- levels(dge$samples$cluster)

Top20DE

$`Amacrine cells`
             logFC   AveExpr         t      P.Value    adj.P.Val           B
HES6     137.79036 5.7313289 21.572562 6.400428e-41 8.372400e-37 36.66520153
DLL3     106.14625 4.3088770 19.907780 6.595993e-38 4.314110e-34 19.06034200
RGS16    118.68794 4.9943264 17.838842 5.909533e-34 2.576753e-30 24.65266014
SRRM4    133.30135 1.8829324 17.682755 1.200199e-33 3.924950e-30 10.31711616
INSM1    124.37961 1.9175950 16.849282 5.559195e-32 1.454396e-28  7.80697749
PSTPIP1  120.58200 1.2632228 16.777183 7.778568e-32 1.695857e-28  5.80279816
CBFA2T2   78.54404 4.3140507 16.615207 1.658373e-31 3.099025e-28 10.47993920
NHLH1    144.63398 2.4191008 16.173774 1.327261e-30 2.170238e-27 14.33899449
NEUROG1  182.46252 1.7460017 15.783740 8.507417e-30 1.199075e-26 17.45748702
FAM110A  103.63326 4.1012229 15.768156 9.166537e-30 1.199075e-26 13.35966764
NEUROD4  153.79389 1.0191708 14.875452 6.914986e-28 8.223176e-25  8.88826045
SSTR2    105.53379 3.4229741 14.787729 1.062928e-27 1.158680e-24 10.84231901
ELAVL3   120.97024 2.1343713 14.558902 3.276134e-27 3.296546e-24  7.36663914
GADD45G   89.87789 5.2897434 14.531386 3.752484e-27 3.506160e-24 16.77335790
NEUROD1  159.67596 1.6536858 14.442950 5.808491e-27 5.065391e-24 12.00067309
SEPTIN4  114.57766 1.7687265 14.155182 2.421594e-26 1.979805e-23  4.63078097
KIF19    136.37895 1.3771939 13.758754 1.756514e-25 1.351586e-22  5.57631803
ELAVL2   110.44799 2.7520644 13.676437 2.656080e-25 1.930233e-22  7.91156179
TFDP2     48.43140 6.4077907 13.166614 3.492107e-24 2.404224e-21 11.89863059
CHRNA3   117.42927 1.3963072 13.074253 5.584008e-24 3.652221e-21  3.44845740
EYA2     135.97013 1.6854637 12.944092 1.083472e-23 6.749000e-21  6.30965066
CLDN5    134.00845 1.3795725 12.527914 9.111648e-23 5.417703e-20  3.61751478
CACNA1A   91.11103 3.3103615 12.449231 1.365030e-22 7.763463e-20  4.96120745
SUSD2    131.07225 1.2870609 12.344459 2.340040e-22 1.275419e-19  3.36822646
CHRNA1   134.59861 0.2572580 11.971511 1.604481e-21 8.311963e-19  1.14723887
ZBTB18    87.87361 3.1687646 11.965860 1.652099e-21 8.311963e-19  4.60210476
DCX      107.52978 2.6276693 11.698102 6.620392e-21 3.207457e-18  5.16325889
EBF2     115.03242 1.5961777 11.604852 1.074673e-20 5.020642e-18  2.61195517
PLXNA1    60.06854 4.2379731 11.468423 2.185062e-20 9.856137e-18  3.35695266
CBFA2T3   92.16034 1.8429963 11.366912 3.707202e-20 1.616464e-17  0.50323017
ADGRA1   105.40870 0.8505363 10.841656 5.755227e-19 2.428520e-16 -0.32796806
IGFBPL1   92.38602 3.9587682 10.785613 7.715860e-19 3.154099e-16  6.76831057
FAM189A1 103.61750 0.4404570 10.732108 1.020877e-18 4.046695e-16 -0.88522790
MYCL      90.78804 2.8830861 10.688653 1.281581e-18 4.930694e-16  2.37783187
KIF1A     80.35540 3.9084460  9.818616 1.221861e-16 4.566617e-14  3.30445636
SH2D5     95.65907 0.7321807  9.242955 2.476931e-15 9.000206e-13 -1.60347905
RASGEF1B  73.42071 2.9083221  9.174861 3.532610e-15 1.248921e-12  0.24750260
TAGLN3   101.27309 3.8492674  9.144134 4.146037e-15 1.427219e-12  5.38671194
SYP       96.44702 1.8687858  9.025861 7.674561e-15 2.574127e-12 -0.32444743
UBE2L6    68.91058 4.9988187  9.005012 8.553695e-15 2.797272e-12  4.94041924
TFAP2C    97.94158 2.4365566  8.835238 2.066244e-14 6.592326e-12  1.13693308
CHRNB4    93.49576 0.2301937  8.760924 3.037632e-14 9.460778e-12 -1.90929720
UNCX     102.25161 0.8871815  8.676436 4.704896e-14 1.431273e-11 -1.22774447
PCBP4     79.97810 5.4426251  8.526336 1.021922e-13 3.022877e-11  6.32789589
DCC      105.98570 2.0332127  8.522956 1.039901e-13 3.022877e-11  0.59071391
TUBB2B    39.21269 8.1127821  8.483002 1.277876e-13 3.614259e-11  8.88169868
SPSB4     76.83020 3.1235051  8.479881 1.298602e-13 3.614259e-11 -0.01000446
PHF21B    73.47780 2.8678129  8.438064 1.610875e-13 4.389970e-11 -0.57735478
RAPGEF5   75.11014 2.4265624  8.433094 1.652649e-13 4.411899e-11 -0.78903859
CDH15    106.92305 1.0108015  8.403748 1.922201e-13 5.028863e-11 -1.34821426

$Cardiomyocytes
             logFC    AveExpr        t      P.Value    adj.P.Val        B
MYL7     130.66430  3.0976950 30.21845 1.847703e-54 2.416980e-50 46.30499
BMP4     100.17794  4.6916506 26.04480 2.482904e-48 1.244905e-44 47.33820
MYL4     128.60340  3.2151048 26.00579 2.855068e-48 1.244905e-44 43.38726
CYB5D1    83.34643  3.8300429 25.22105 4.896782e-47 1.601370e-43 38.70436
APOBEC3G  90.85741  2.0962458 23.72382 1.325661e-44 3.240680e-41 27.97143
DOK4      71.25664  4.8213956 23.69388 1.486437e-44 3.240680e-41 41.78124
CFC1     100.08962  1.1041893 22.03796 9.765033e-42 1.824806e-38 23.39502
HS3ST3A1  86.60612  2.1116755 21.92962 1.509262e-41 2.467832e-38 26.51592
GLIPR2    73.08017  3.9350171 21.68732 4.016454e-41 5.837692e-38 35.41663
BAG3      58.11844  4.2447476 21.03112 5.891112e-40 7.706163e-37 33.46104
FGF19    107.72012  2.2553657 20.82809 1.366447e-39 1.624954e-36 29.36165
BMPER     96.84503  2.3372969 20.16516 2.207314e-38 2.406156e-35 28.62389
TNNT2     92.88780  2.9350416 20.11749 2.701837e-38 2.718672e-35 30.65986
COBLL1    66.26504  3.8078148 18.55705 2.360551e-35 2.205597e-32 28.89878
DNAH2     87.33649  1.5861408 18.34031 6.195401e-35 5.402803e-32 20.95438
KRT19     65.97059  8.6797897 18.26668 8.610261e-35 7.039426e-32 49.52404
PLPPR5    84.77348  1.3670778 18.18679 1.231576e-34 9.476617e-32 18.83396
TMOD1     83.64226  1.9293714 18.15105 1.445832e-34 1.050718e-31 21.66704
PSKH2    102.71186  0.5888992 18.12316 1.638795e-34 1.078437e-31 18.74104
APLNR    121.89089  2.3444355 18.12179 1.648860e-34 1.078437e-31 29.79227
TMEM185A  53.09470  3.9425363 18.02878 2.505759e-34 1.506125e-31 27.13528
TNNI1    121.51287  3.9575031 18.02637 2.533044e-34 1.506125e-31 35.69392
RGS13    144.64986  2.6808708 17.99972 2.856335e-34 1.568971e-31 32.12976
HTRA1     80.66431  3.5987240 17.99800 2.878626e-34 1.568971e-31 29.75697
PRDM6     81.90209  1.8387960 17.78189 7.650104e-34 4.002840e-31 20.50841
LHFPL2    51.42098  3.8578678 17.43567 3.707501e-33 1.865301e-30 25.51257
ALPK2     86.60294  2.0494678 17.39412 4.485349e-33 2.173068e-30 22.24025
HAND1    134.92284  4.6368572 17.30063 6.890111e-33 3.218912e-30 37.49295
LYN       58.36667  3.5424557 17.05154 2.174038e-32 9.806410e-30 24.28785
SVEP1     71.29496  2.2052858 16.82727 6.159146e-32 2.685593e-29 19.22263
BAMBI     74.02825  6.5277939 16.79757 7.073195e-32 2.984660e-29 39.16688
SLC9A3R1  45.81782  6.6814823 16.76133 8.375453e-32 3.423728e-29 36.82614
HAS2      87.30497  5.5998335 16.66846 1.292503e-31 5.102493e-29 36.31877
ACTC1    112.70701  5.6095105 16.66295 1.326235e-31 5.102493e-29 40.55194
FABP5     58.77926  7.8679014 16.54164 2.341450e-31 8.751003e-29 44.09118
S100A11   45.05607 10.0171268 16.52148 2.573913e-31 9.352597e-29 48.96027
SHISAL2B  73.73926  2.6002339 16.10512 1.838141e-30 6.498575e-28 20.38247
TCF21     85.51477  1.8131395 15.90283 4.814762e-30 1.657419e-27 18.99167
FAM89A    76.32724  5.8430913 15.81296 7.397133e-30 2.481074e-27 36.12206
GYPB     109.95160  0.4211041 15.66734 1.486511e-29 4.861262e-27 16.12666
PPFIBP1   40.37845  5.1133169 15.50954 3.175936e-29 1.013279e-26 27.98998
TUBB6     57.58937  5.2111883 15.47312 3.785710e-29 1.179069e-26 29.67380
ADAM19    68.91500  3.7111987 15.43315 4.591396e-29 1.396745e-26 24.78315
ADGRA2    71.74334  2.0801881 15.35020 6.856677e-29 2.036366e-26 17.12242
HAPLN1   135.31468  5.1626583 15.34577 7.005309e-29 2.036366e-26 35.92405
MIXL1    109.03120  2.2806485 15.11656 2.131129e-28 6.060284e-26 22.94231
P3H2      58.24763  3.7355420 14.89919 6.156338e-28 1.713427e-25 22.47444
RGS5      89.58711  5.7892420 14.89128 6.399314e-28 1.743946e-25 33.65425
KDR       86.16713  2.9812211 14.69530 1.673609e-27 4.467853e-25 22.30438
HOXB6    110.90093  2.6245312 14.68790 1.735630e-27 4.540755e-25 24.16276

$`Ciliated epithelial cells`
             logFC     AveExpr        t      P.Value    adj.P.Val         B
CCNO     163.23030  1.34197803 28.29687 1.005253e-51 1.314971e-47 31.826614
CFAP126  157.20135  1.28110739 22.91650 3.006389e-43 1.966329e-39 26.502261
C11orf88 123.24933  0.46093334 19.25926 1.078980e-36 4.704714e-33 12.773345
CDC20B   123.27765  0.91970265 18.98852 3.519398e-36 1.150931e-32 17.650908
MLF1      55.05400  5.48825432 17.85601 5.467436e-34 1.430391e-30 26.357689
TEKT1    110.48383  0.16108534 17.20423 1.073871e-32 2.341217e-29  7.676046
RSPH1    107.49748  1.15679651 16.86721 5.114186e-32 9.556952e-29 11.343925
KIF9      65.33544  4.06698819 16.56006 2.147585e-31 3.511570e-28 18.282823
ROPN1L    94.85894  0.52961491 16.34023 6.041077e-31 8.780369e-28  6.491970
C1orf189  97.43277  0.31886971 16.11162 1.782348e-30 2.170743e-27  6.356314
SOX2      87.04185  4.91896284 16.10659 1.825409e-30 2.170743e-27 26.622024
FAM183A   99.33717  1.54378909 15.95431 3.766610e-30 4.105919e-27 11.991038
FOXJ1    104.97174  2.23512164 15.89446 5.011113e-30 5.042336e-27 15.726576
MUC12     80.37503  3.00255390 15.80142 7.817328e-30 7.304176e-27 15.007015
SPEF1     95.35842  0.75877560 15.66342 1.514734e-29 1.320949e-26  7.427261
C1orf194 120.85931  0.98385779 15.46962 3.850163e-29 3.147749e-26 12.530443
CCDC39    95.41475  0.66244041 14.99746 3.808497e-28 2.930526e-25  6.777590
MAP3K19   94.07040 -0.01846654 14.70544 1.592225e-27 1.157105e-24  4.116229
CAPSL    101.38635  0.29807548 14.60015 2.673245e-27 1.820235e-24  5.314272
PIFO      87.40241  3.52882807 14.59199 2.783022e-27 1.820235e-24 16.545988
CFAP52    98.63289  0.23664402 14.49739 4.438290e-27 2.764632e-24  5.085500
C9orf24   97.31268  1.05337208 13.97438 5.965985e-26 3.547320e-23  6.942407
SFRP2     74.81157  4.98786079 13.57246 4.482570e-25 2.549413e-22 20.428848
TPPP3    109.06701  2.54630137 13.46312 7.780949e-25 4.240941e-22 15.177708
FAM81B   107.60643  0.48102623 13.35301 1.357530e-24 7.103139e-22  6.193938
SPAG1     77.97744  2.54006124 12.94140 1.098461e-23 5.526528e-21  8.760483
CFAP45   106.88074  0.76783517 12.89760 1.373436e-23 6.654044e-21  6.654259
SPAG6    106.34559  0.76710346 12.45053 1.355917e-22 6.334553e-20  5.861414
C20orf85  96.91822 -0.03038045 12.35423 2.225274e-22 1.003752e-19  3.419779
ZMYND10  104.00875  0.99718113 12.29681 2.990935e-22 1.304147e-19  6.610048
SPAG8     87.20679  0.73978223 12.20234 4.867666e-22 2.053998e-19  3.698165
DAW1      84.03744  0.39915960 11.75468 4.935570e-21 2.017569e-18  2.294866
PLEKHA5   35.56665  6.47976484 11.72958 5.622365e-21 2.228671e-18 17.407452
SPAG17    82.38803  1.51749551 11.71134 6.180585e-21 2.377889e-18  5.087372
CCDC170   76.61496  0.62621966 11.56523 1.320524e-20 4.935365e-18  2.156678
RFX3      50.81374  4.23170857 11.55051 1.425561e-20 5.179934e-18 10.015639
C5orf49  101.88563  1.94581738 11.52209 1.652612e-20 5.842655e-18  9.088395
TPBG      91.29992  6.17059639 11.27743 5.910331e-20 2.034554e-17 21.753149
RSPH4A    99.14527  1.04673557 11.19386 9.139565e-20 3.065504e-17  5.628114
MCUB      65.42028  3.61777699 11.15422 1.123974e-19 3.675677e-17  8.240501
CCDC114   82.49538  0.38231633 11.04939 1.943020e-19 6.199181e-17  1.662925
DRC1     107.58455  0.80926145 10.83577 5.935310e-19 1.848567e-16  4.826680
IGFBPL1   69.22922  3.95876817 10.74157 9.715524e-19 2.955553e-16 11.661006
WDR49     91.96656  0.44017013 10.66534 1.447915e-18 4.304584e-16  2.605762
AKAP14    80.99571  0.27168377 10.56856 2.403258e-18 6.986003e-16  1.365864
LRRC73    72.98617  1.68691586 10.42588 5.074221e-18 1.442954e-15  2.994006
PLXDC2    53.37388  3.92130700 10.41727 5.308163e-18 1.477363e-15  7.161856
DNAH7     85.80930  0.95375866 10.36158 7.106661e-18 1.936713e-15  3.075866
EFHC1     52.83757  4.46622294 10.31434 9.102208e-18 2.429918e-15  9.754151
BMP7      47.07608  4.37485330 10.18567 1.786249e-17 4.673184e-15  7.989635

$`Ductal cells`
             logFC   AveExpr        t      P.Value    adj.P.Val         B
SHH      143.68142 0.7005265 24.00904 4.476841e-45 5.856156e-41 25.484185
GASK1B   111.42556 1.9409450 21.82597 2.292073e-41 1.499130e-37 26.162351
IHH      110.65252 1.5264822 20.63833 3.013624e-39 1.314041e-35 21.719632
TMEM229A 104.30223 1.2756792 19.34869 7.316162e-37 2.392568e-33 18.251292
FOXA2    114.43579 2.3626344 19.23913 1.177750e-36 3.081229e-33 26.428385
MNX1     105.60992 1.5673352 18.50659 2.953525e-35 6.439177e-32 19.380783
VIL1      87.36363 2.0194712 18.42958 4.160683e-35 7.775128e-32 18.740219
CST1     167.14941 3.0632741 18.14218 1.504589e-34 2.460192e-31 33.779978
CST4     129.03536 1.5048488 17.79236 7.295442e-34 1.060352e-30 23.122807
HPGD      92.90406 2.5690598 17.02789 2.425680e-32 3.173032e-29 22.107840
RAB25     86.89581 3.8125574 16.98471 2.963137e-32 3.523708e-29 27.763366
FOXA1     96.01516 1.2318728 16.80737 6.757564e-32 7.366308e-29 15.085899
SCGB1A1  102.34758 0.1694337 16.59235 1.845871e-31 1.857372e-28 13.048433
FOXQ1    106.89928 2.0403927 16.43284 3.904432e-31 3.648134e-28 19.755407
WFDC2     72.85817 5.5491577 16.02459 2.695232e-30 2.350422e-27 32.892269
ALPL      66.50418 3.8378051 15.72366 1.134488e-29 9.275149e-27 22.147217
KLF5      73.47058 2.4044719 15.53447 2.816366e-29 2.167111e-26 16.140863
CLDN3     70.70027 3.3835805 15.17622 1.594377e-28 1.158669e-25 20.649345
NENF      80.20328 6.4620381 14.69911 1.642583e-27 1.130875e-24 34.223838
SMAGP     57.94867 3.4949297 14.59426 2.752014e-27 1.799955e-24 17.329190
CAPN9     95.35551 1.0291877 14.36429 8.573447e-27 5.340441e-24 11.712069
CDH17     89.86364 0.1431509 14.27014 1.367541e-26 8.131274e-24  7.208636
IGFBP6    89.25511 2.7075884 14.21563 1.792784e-26 1.019626e-23 18.687988
ZFP36L2   56.75904 6.5312268 14.19452 1.991200e-26 1.085287e-23 30.061186
ARHGEF19  55.80740 2.8774848 14.09315 3.298280e-26 1.725491e-23 14.028964
SLC12A2   50.63194 4.6590684 14.08531 3.429614e-26 1.725491e-23 21.783638
EPCAM     96.33657 5.6005879 14.01170 4.951503e-26 2.398912e-23 29.962477
ANXA3     76.35277 4.3416845 13.97558 5.930321e-26 2.770519e-23 23.446413
CLDN4     92.06373 2.9275341 13.96752 6.173848e-26 2.784831e-23 20.501571
SOX17    132.40726 2.5971138 13.95660 6.520269e-26 2.843055e-23 21.945171
KRT18     59.37421 8.5293745 13.92361 7.689691e-26 3.243472e-23 35.272731
DSP       56.27506 7.0748749 13.91734 7.934493e-26 3.243472e-23 31.084035
ECHDC1    32.50908 6.5067194 13.82183 1.280131e-25 5.074363e-23 26.964859
TNNC1     78.28109 4.0471838 13.77244 1.639945e-25 6.309447e-23 22.462253
TRIM17    78.80793 2.2665971 13.69481 2.421820e-25 9.051379e-23 13.310627
KITLG     77.52114 2.8648700 13.58284 4.254059e-25 1.545760e-22 14.802235
C10orf82  60.12093 2.9468109 13.57226 4.486955e-25 1.586320e-22 14.369047
SERPINI1  60.40501 3.1162122 13.48031 7.134108e-25 2.455823e-22 14.076346
FREM2     61.54915 3.9451632 13.46815 7.585900e-25 2.544389e-22 19.039074
GJA4      86.58513 1.4068779 13.36670 1.266669e-24 4.142326e-22 10.562944
F2        75.96756 1.0658412 13.19079 3.088712e-24 9.854499e-22  7.941239
SAT1      62.05157 6.3992827 13.18354 3.204519e-24 9.980550e-22 28.732950
SGK1      78.82008 2.0537412 13.04839 6.369178e-24 1.937563e-21 12.001188
SH3YL1    41.29040 4.4045214 12.92805 1.175834e-23 3.495702e-21 17.556978
APOA2     87.99515 4.5700960 12.82426 1.997231e-23 5.805727e-21 21.578721
TMEM54    54.18468 3.5830793 12.80886 2.160715e-23 6.144417e-21 15.814817
DEFA5     95.13129 0.4415613 12.77085 2.624180e-23 7.303596e-21  7.902071
FBLN2     61.42286 4.0725440 12.71361 3.516942e-23 9.584400e-21 17.632106
PCBD1     33.40965 6.9252945 12.64991 4.873590e-23 1.301050e-20 25.673380
SHISAL2B  66.63326 2.6002339 12.57839 7.032133e-23 1.839747e-20 12.248142

$`Epicardial fat cells`
             logFC   AveExpr        t      P.Value    adj.P.Val         B
SLC9A3R1  94.32841 6.6814823 31.17107 9.138907e-56 1.195460e-51 49.580065
AQP1     164.03920 1.8756794 29.33866 3.175444e-53 2.076899e-49 31.780688
COBLL1   110.26270 3.8078148 28.06091 2.228486e-51 9.716943e-48 32.216841
ANXA8    139.36332 0.8855355 23.88767 7.097668e-45 2.321115e-41 18.947166
TNNT2    121.16601 2.9350416 22.04344 9.552540e-42 2.499136e-38 25.527118
SERPINE3 157.28547 0.3786379 21.35077 1.582165e-40 3.449383e-37 18.580813
CARD16   130.10506 0.4869025 20.78315 1.647295e-39 3.078323e-36 13.798601
SLC40A1  120.91422 3.3828801 20.33706 1.067363e-38 1.745271e-35 26.954025
FIBIN    120.34115 1.8971410 19.80080 1.042173e-37 1.400640e-34 18.273241
SLC5A12  122.43393 2.7850221 19.79448 1.070744e-37 1.400640e-34 23.247790
SLC34A2  134.51562 0.5276665 19.63829 2.093532e-37 2.489590e-34 13.149710
FRZB     135.29174 5.4381793 19.52031 3.480986e-37 3.794565e-34 37.826990
SLN      172.16274 2.2626310 19.17227 1.575945e-36 1.585764e-33 28.166227
SARAF     47.45876 7.8538281 19.12684 1.921526e-36 1.795391e-33 36.328088
CD44     105.09442 2.5102088 18.87231 5.862353e-36 5.112363e-33 17.213029
KRT24    125.83223 0.6689462 18.37455 5.317432e-35 4.347333e-32 12.817443
SLC7A7   113.14202 2.5859236 18.28548 7.915664e-35 5.756301e-32 19.029768
LIMS1     50.07334 6.2651233 18.28534 7.920909e-35 5.756301e-32 27.400972
MYRF      91.47066 3.1829695 17.66979 1.273151e-33 8.765307e-31 17.221080
NPNT     112.80533 2.4641667 17.50080 2.751941e-33 1.799907e-30 17.464960
ATP7B     89.64066 3.0250264 17.47059 3.159827e-33 1.968271e-30 15.340508
COL1A1   115.44418 6.2764999 17.25933 8.331386e-33 4.953767e-30 34.605028
MYL4     115.74911 3.2151048 17.22731 9.655107e-33 5.491237e-30 22.472821
AKR1B15  112.24352 1.5067348 17.00306 2.721502e-32 1.483332e-29 12.536939
RAMP1    104.13799 3.0053905 16.95251 3.440539e-32 1.767709e-29 18.412173
LUM      152.36937 4.7155844 16.94799 3.513525e-32 1.767709e-29 31.194031
AEBP1     66.19705 4.4020690 16.70945 1.067099e-31 5.169897e-29 17.839711
DSC3      96.44074 1.9939554 16.56494 2.098997e-31 9.806063e-29 10.997464
BNC1     109.40344 1.2420685 16.47173 3.251676e-31 1.466730e-28 10.605918
IFIT1     97.15666 3.0191987 16.33195 6.281854e-31 2.739098e-28 16.400664
STX18     53.61765 5.5193489 16.31759 6.722296e-31 2.836592e-28 21.996926
DCN      170.29764 3.1437291 16.24605 9.426333e-31 3.853308e-28 26.585083
PRCD     101.98930 1.8232319 16.03631 2.549072e-30 1.010437e-27 10.994048
PRSS35   104.46662 3.2397555 15.76657 9.236339e-30 3.553546e-27 17.902110
TGFBR3    83.13219 3.1869881 15.66822 1.480237e-29 5.401942e-27 14.315488
THBD     109.86076 1.2038102 15.66732 1.486659e-29 5.401942e-27  9.497693
CYB5R2    71.65741 3.6845580 15.44968 4.239161e-29 1.498715e-26 14.138403
FMO1     121.00192 1.8281981 15.43197 4.617548e-29 1.589530e-26 13.891087
TNFAIP3   83.59592 2.5601386 15.42171 4.852378e-29 1.627537e-26 11.006959
LEPROTL1  46.89480 6.6570553 15.35822 6.595722e-29 2.156966e-26 24.997326
COL8A2   113.61595 0.8062160 15.20363 1.395583e-28 4.452591e-26  8.202056
CREB3L1   91.05316 3.4812380 15.17808 1.580030e-28 4.921040e-26 15.947947
COL21A1  106.65926 2.4613167 15.11512 2.146139e-28 6.528756e-26 13.909096
DDR2      99.44669 2.8971187 14.95038 4.793167e-28 1.424987e-25 14.809412
BNC2      90.04942 3.2479340 14.77729 1.118775e-27 3.252155e-25 14.694171
COL5A1    89.20959 4.4965267 14.68603 1.751697e-27 4.981292e-25 20.371664
COL3A1   145.76480 5.3883411 14.50923 4.186286e-27 1.165124e-24 28.085792
POSTN    144.74872 3.8513366 14.46962 5.091088e-27 1.387428e-24 23.648476
GALNT10   71.67659 3.8606737 14.29188 1.227626e-26 3.277261e-24 14.009655
MORC4     61.06956 3.6446214 14.19274 2.008873e-26 5.255613e-24 10.606694

$`Goblet cells`
             logFC   AveExpr        t      P.Value    adj.P.Val        B
CCKBR    110.06733 2.8864382 27.13638 5.299746e-50 6.932597e-46 34.45488
FAM184A  111.18722 3.7029690 26.59280 3.547390e-49 2.320171e-45 39.16682
CCDC81   112.89029 2.0075884 24.57342 5.362603e-46 2.338274e-42 28.75924
FOXA2    135.58586 2.3626344 24.36400 1.173844e-45 3.838765e-42 33.43206
PLSCR2   156.23423 1.2118813 22.46276 1.794525e-42 4.694836e-39 30.53716
FOXQ1    127.32312 2.0403927 22.17410 5.660983e-42 1.234189e-38 29.48584
EPSTI1    90.64317 3.4167152 21.75971 2.995958e-41 5.598589e-38 30.13592
PRSS1    131.85935 0.8334319 21.55212 6.955368e-41 1.137290e-37 23.75502
WFDC2     94.70063 5.5491577 21.13068 3.906486e-40 5.677861e-37 42.06517
PDZK1    103.45192 1.2293187 20.59803 3.566782e-39 4.665707e-36 19.35213
HHEX     122.18081 1.3410679 19.98705 4.704070e-38 5.593995e-35 23.16529
MNX1     107.41996 1.5673352 19.74719 1.311325e-37 1.429454e-34 21.93046
CST1     179.17866 3.0632741 19.60511 2.414928e-37 2.429975e-34 36.22476
PCBD1     50.64427 6.9252945 19.25038 1.121471e-36 1.047855e-33 39.82232
CER1     127.15289 2.0397658 19.22920 1.229750e-36 1.072424e-33 26.75497
APOA2    119.66504 4.5700960 19.20541 1.363996e-36 1.115152e-33 35.90340
ADM       92.94778 2.6525145 18.53301 2.626421e-35 2.020954e-32 23.25370
COCH      78.55069 2.9374724 18.51580 2.835125e-35 2.060348e-32 21.82873
VIL1      87.76423 2.0194712 18.00399 2.801959e-34 1.916170e-31 17.55428
PRSS2    147.93660 1.1202828 17.99410 2.929700e-34 1.916170e-31 24.34888
LGR5     100.62783 2.0058344 17.85650 5.455356e-34 3.398167e-31 20.82498
HP        91.12315 0.7621428 17.23865 9.163674e-33 5.448637e-30 12.36840
PRDM1     86.35157 2.2010891 16.94614 3.543894e-32 2.015551e-29 17.77801
LAPTM4B   41.72772 8.8668685 16.83053 6.066454e-32 3.306470e-29 42.72303
SEMA3E    99.20815 2.3329429 16.72611 9.871974e-32 5.165412e-29 21.32080
GSC      114.41262 1.2115720 16.69491 1.142154e-31 5.746352e-29 18.44214
TRDN     116.24882 2.4302318 16.62183 1.607734e-31 7.789176e-29 23.68620
GATA4     89.42945 2.7684350 16.61108 1.690749e-31 7.898819e-29 21.20670
APOC1     67.04166 6.5875047 16.41397 4.267182e-31 1.924794e-28 34.17720
P3H2      68.58017 3.7355420 16.35614 5.604186e-31 2.443612e-28 22.42240
PIK3R5    98.47909 1.0060652 16.20222 1.159931e-30 4.894535e-28 13.88334
SLC2A3    78.14671 6.2843433 15.97168 3.467387e-30 1.417403e-27 33.92845
CARHSP1   30.78005 7.6020921 15.92244 4.384780e-30 1.738100e-27 33.87210
SOX17    144.19265 2.5971138 15.72429 1.131055e-29 4.351569e-27 25.92978
FZD5     124.92947 2.5612493 15.60152 2.039471e-29 7.622378e-27 23.92463
PTGR1     63.85621 7.4625797 15.35187 6.801564e-29 2.471424e-26 36.45198
IHH       92.79370 1.5264822 15.29866 8.800670e-29 3.111393e-26 13.79140
RAB25     84.74324 3.8125574 15.28362 9.466381e-29 3.258677e-26 22.72676
SHISAL2B  77.09117 2.6002339 15.21107 1.346002e-28 4.514628e-26 16.47193
KCNK12    92.47674 2.3998878 15.11194 2.179672e-28 7.128072e-26 18.01654
PLCXD3    78.63658 1.3469952 15.06235 2.775100e-28 8.853922e-26 10.88065
S100A16   72.61461 4.6850373 14.47149 5.044063e-27 1.544670e-24 23.35201
VAMP8     63.76696 5.2537599 14.47015 5.077655e-27 1.544670e-24 24.95638
SLCO2A1   78.39423 1.7276243 14.10620 3.090593e-26 9.188192e-24 11.76974
DMKN      72.43869 6.0650201 13.99308 5.433838e-26 1.579556e-23 27.86286
TFF3     106.42073 1.2060964 13.88830 9.175538e-26 2.609244e-23 13.06430
NRG1      67.79722 3.1473479 13.83526 1.196784e-25 3.330879e-23 16.57545
SERPINE2  76.13986 6.3636276 13.77987 1.579945e-25 4.305679e-23 28.51404
DENND2C   81.87393 2.2918567 13.71887 2.145970e-25 5.728865e-23 13.85858
FOXA1     86.35555 1.2318728 13.69756 2.388560e-25 6.220098e-23 10.05577

$`Granule neurons`
            logFC   AveExpr        t      P.Value    adj.P.Val        B
ELAVL3  156.33323 2.1343713 32.36363 2.347957e-57 2.446583e-53 33.67212
LHX9    167.85888 2.0780892 32.20993 3.740666e-57 2.446583e-53 35.76887
UNCX    162.10375 0.8871815 31.87166 1.049182e-56 4.574782e-53 26.49825
INSM1   140.90935 1.9175950 30.55843 6.265015e-55 2.048816e-51 27.84146
NHLH1   177.85335 2.4191008 30.28651 1.486868e-54 3.889944e-51 39.68953
IGFBPL1 136.12734 3.9587682 27.91827 3.614750e-51 7.880757e-48 40.30392
ST18    155.66791 0.5091356 27.64646 9.133926e-51 1.664765e-47 20.29504
KLHL35  141.33031 2.1556421 27.61476 1.018127e-50 1.664765e-47 28.66000
TLCD3B  139.20300 1.7731339 27.53008 1.361277e-50 1.978541e-47 24.09398
KIF5C   112.28194 4.4306399 25.35045 3.051426e-47 3.991570e-44 36.74672
EBF3    135.22512 1.2507997 24.84783 1.934684e-46 2.300691e-43 19.04715
DLL3     98.38386 4.3088770 24.71690 3.143596e-46 3.426781e-43 33.55651
DCX     134.38971 2.6276693 24.42075 9.488791e-46 9.547914e-43 28.50277
CRMP1   112.53436 3.7555245 24.33749 1.296674e-45 1.211556e-42 30.41818
INA     114.57696 2.6686304 24.12829 2.851098e-45 2.486348e-42 23.18005
SYP     130.93550 1.8687858 24.05421 3.772801e-45 3.084500e-42 21.57818
CELF3   133.83305 1.2546600 23.83143 8.792364e-45 6.765465e-42 17.73571
TAGLN3  148.73051 3.8492674 23.60610 2.080385e-44 1.511862e-41 39.31041
DRAXIN  102.70779 3.3897111 23.27939 7.324726e-44 5.042881e-41 24.57928
OLFM1   117.16334 2.7883832 23.11455 1.388522e-43 9.081628e-41 24.84213
MAP1B    79.33089 8.7464887 22.93908 2.752263e-43 1.714398e-40 55.77921
ELAVL2  122.53480 2.7520644 22.61322 9.897444e-43 5.884930e-40 25.61333
SSTR2   109.70176 3.4229741 21.64626 4.744313e-41 2.698277e-38 26.61585
STMN2   146.68650 4.7054494 21.55954 6.748672e-41 3.678307e-38 41.85128
CNTN2   143.86429 1.5307494 21.47216 9.634296e-41 5.041049e-38 21.80347
EBF2    130.72138 1.5961777 21.44444 1.078814e-40 5.427678e-38 18.91179
INSM2   139.33855 0.3073516 21.43179 1.136007e-40 5.503743e-38 11.97642
GNG3    101.76171 2.6673015 21.14580 3.670578e-40 1.714815e-37 17.63171
DCC     141.76902 2.0332127 21.05629 5.309289e-40 2.394855e-37 23.52783
TCP10L  108.81063 1.7550309 20.97527 7.421458e-40 3.236003e-37 13.49612
CFAP298  70.70351 6.2406198 20.63205 3.093708e-39 1.305445e-36 36.00796
HES6    113.71186 5.7313289 20.46766 6.160804e-39 2.518421e-36 41.01402
RTN1    124.62127 3.1365014 20.36582 9.455307e-39 3.748027e-36 26.37755
ADCYAP1 126.32955 0.8113424 20.25883 1.485007e-38 5.713345e-36 12.09939
TUBB2B   60.57004 8.1127821 19.98654 4.714264e-38 1.761922e-35 43.28248
MLLT11   71.95415 7.5497265 18.94765 4.210281e-36 1.529853e-33 41.32164
NEUROD1 159.60363 1.6536858 18.77878 8.850720e-36 3.129088e-33 23.65809
CCNO    142.98429 1.3419780 18.71684 1.163368e-35 4.004742e-33 16.12188
NRXN1   116.52061 2.7210766 18.34759 5.997303e-35 2.011557e-32 19.62318
SCG3    125.34658 2.9950166 18.16603 1.351788e-34 4.420684e-32 23.41934
RGS16   100.52619 4.9943264 17.95143 3.551671e-34 1.133156e-31 30.80409
TBR1    150.83697 0.6804992 17.81831 6.485756e-34 2.020004e-31 14.94161
NHLH2   104.28010 1.9647414 17.25003 8.696093e-33 2.645432e-30 11.73556
CALY    104.26306 2.8062889 17.19998 1.095136e-32 3.255789e-30 16.53923
NPTX2   113.24127 1.6393260 17.15161 1.368920e-32 3.979299e-30 10.93535
SRRM4   110.62813 1.8829324 16.95499 3.401226e-32 9.672051e-30 13.43849
RORB    127.85261 1.2607454 16.78292 7.573349e-32 2.107808e-29 11.94338
FNDC5   100.77977 2.9112692 16.76738 8.142510e-32 2.219004e-29 16.37960
RAB26   104.73355 1.9711739 16.69505 1.141405e-31 3.047086e-29 11.38274
CACNA1A  87.09858 3.3103615 16.66791 1.295838e-31 3.390171e-29 15.27027

$Hepatoblasts
             logFC      AveExpr        t      P.Value    adj.P.Val        B
APOB     212.86304  2.418662449 68.74141 6.875979e-91 8.994469e-87 58.83317
RBP4     240.42874  2.706134932 65.40843 1.291711e-88 6.583320e-85 63.74390
AHSG     236.55900  1.178939669 65.31151 1.509820e-88 6.583320e-85 53.12502
AFP      239.64321  2.782945774 64.82664 3.306424e-88 1.081283e-84 63.19406
FGA      220.48744  1.156850499 62.39136 1.847634e-86 4.833781e-83 51.18439
APOC3    243.09001  2.002620895 57.22719 1.568987e-82 3.420652e-79 57.89520
SMLR1    178.81594  1.189693142 57.11940 1.910453e-82 3.570091e-79 45.63108
GSTA2    193.54753  1.867321844 56.98326 2.451045e-82 4.007766e-79 51.72488
FGG      224.47363  1.260810569 55.93150 1.712504e-81 2.489030e-78 51.28503
FGB      236.11890  1.690912416 53.10761 3.766354e-79 4.926768e-76 54.68095
APOM     163.46578  3.604052826 53.04605 4.248771e-79 5.052561e-76 59.21709
G0S2     208.17758  2.071547317 51.92153 3.929938e-78 4.283960e-75 54.20816
SERPINA1 225.53980  0.926589202 51.80391 4.972186e-78 5.003166e-75 49.84857
LGALS2   168.44205  0.845959810 48.62786 3.462019e-75 3.084435e-72 40.53230
APOA2    234.91118  4.570095953 48.61777 3.536926e-75 3.084435e-72 69.87807
FABP1    226.38227  1.395422395 48.00378 1.311769e-74 1.072453e-71 50.80848
AGT      174.29327  1.272051385 46.57228 2.959215e-73 2.277029e-70 44.10895
MEP1A    153.38844  0.518379947 45.38133 4.227896e-72 3.072506e-69 34.98358
DPYS     167.01021  0.792165370 45.05930 8.772404e-72 6.039569e-69 39.27715
GLTPD2   145.26622  0.850389220 44.29380 5.068883e-71 3.315303e-68 35.69155
GLUD1     96.74332  5.297080823 44.05679 8.773384e-71 5.464982e-68 59.73280
ASGR2    148.70094  1.089839566 43.50328 3.192191e-70 1.898048e-67 37.76862
MTTP     176.22017  1.291211877 43.35006 4.576000e-70 2.602551e-67 43.06298
DGAT2    125.77295  2.373470168 41.45300 4.352831e-68 2.372474e-65 40.97247
CREB3L3  145.24734  0.408790423 40.81372 2.106213e-67 1.068196e-64 32.18688
ARG1     155.47565  0.198744047 40.81049 2.123163e-67 1.068196e-64 32.94283
APOC1    124.15618  6.587504705 39.87575 2.215231e-66 1.073238e-63 73.35468
AKR1D1   153.81489  0.861641965 39.77276 2.876707e-66 1.343936e-63 36.22255
F2       143.97979  1.065841190 39.72012 3.288511e-66 1.483345e-63 35.75914
SLC39A5  141.60591  0.875527933 39.55897 4.957895e-66 2.161807e-63 33.80627
GPD1     138.49176  0.643634062 39.17875 1.313719e-65 5.543470e-63 31.14492
PRODH2   145.96368  0.336214318 38.73797 4.107670e-65 1.679138e-62 31.79756
AMBP     152.55830  1.117420768 38.65097 5.151042e-65 2.041842e-62 36.91930
ACAA1     82.06253  5.203223501 38.22066 1.588295e-64 6.110731e-62 53.90432
DUSP9    135.92510  1.779731417 37.37224 1.510794e-63 5.646484e-61 37.35442
CEBPA    119.73610  2.361272139 36.34215 2.471104e-62 8.979032e-60 38.22406
SULT1E1  144.65131 -0.004876959 36.14546 4.245791e-62 1.501059e-59 28.71980
GOLT1A   142.67281  1.353479076 35.78202 1.161998e-61 4.000025e-59 35.65822
A1CF     137.11461  0.384271567 35.69544 1.478812e-61 4.960086e-59 29.05437
SLC13A5  137.09125  1.039275002 35.56561 2.124937e-61 6.949074e-59 32.23707
KLB      132.42762  0.706396763 35.53696 2.302242e-61 7.345276e-59 29.30103
SULT2A1  139.06381  0.034109509 35.34683 3.923963e-61 1.222128e-58 26.60808
MPC2      68.41584  7.768511280 35.23282 5.408648e-61 1.645361e-58 71.78758
HNF4A    139.29951  1.216225955 35.08876 8.123476e-61 2.415072e-58 34.85642
GSTA1    172.21517  1.615372085 35.05892 8.838985e-61 2.569395e-58 42.28580
HP       133.73989  0.762142835 34.69744 2.469843e-60 7.023482e-58 30.71709
PLA2G12B 127.67459  1.011311146 34.13228 1.253855e-59 3.489719e-57 30.42250
HPX      137.23671  1.382479304 33.89421 2.502568e-59 6.820020e-57 35.37624
HMGCS2   157.06968  0.987059704 33.82302 3.079407e-59 8.220760e-57 36.17443
DPP4     137.60063  2.059792389 33.65851 4.980269e-59 1.302938e-56 39.17974

$IG
            logFC   AveExpr        t      P.Value    adj.P.Val         B
PCOLCE  107.35012 4.8474419 22.99736 2.192014e-43 2.867374e-39 40.332385
COL1A1  127.72961 6.2764999 22.78231 5.086897e-43 3.327085e-39 50.418184
COL6A2  101.54411 6.2693029 21.43958 1.100416e-40 4.798182e-37 46.113122
COL6A3  131.16234 3.4290288 21.35557 1.551376e-40 5.073386e-37 33.865361
EMILIN1 106.27719 2.8739884 20.58518 3.763778e-39 9.846797e-36 25.467439
TWIST1  116.52184 3.0945849 20.17875 2.083820e-38 4.543075e-35 29.401862
KCTD12   99.51344 3.9630040 18.55580 2.373661e-35 4.435694e-32 28.913021
COL3A1  159.41304 5.3883411 18.42341 4.276534e-35 6.992668e-32 40.676606
DDR2    102.38580 2.8971187 18.39317 4.893657e-35 7.112659e-32 23.623001
COL6A1   72.85261 6.8556861 17.37838 4.820957e-33 6.306294e-30 38.431250
LUM     142.64713 4.7155844 17.13212 1.497838e-32 1.781202e-29 34.084319
COL21A1 102.18611 2.4613167 16.77456 7.874391e-32 8.583742e-29 19.636445
COL1A2   94.94535 6.9908439 16.33419 6.215577e-31 6.254305e-28 39.190941
IGFBP3  122.97875 4.8257654 16.31244 6.887631e-31 6.364335e-28 32.281036
TCF21   102.56134 1.8131395 16.29913 7.334614e-31 6.364335e-28 14.967569
DCN     157.72513 3.1437291 16.28653 7.784524e-31 6.364335e-28 29.185572
PCDH18   71.58878 3.4732442 16.15493 1.451307e-30 1.116738e-27 17.514833
MFAP4   106.23234 4.0818825 16.11096 1.787905e-30 1.299310e-27 27.192346
COL5A1   84.98473 4.4965267 15.91789 4.480961e-30 3.085023e-27 26.072110
NID2     93.61667 3.8234636 15.86680 5.718682e-30 3.740304e-27 23.644215
CD248    92.47414 2.2968251 15.67554 1.429097e-29 8.901911e-27 14.494484
FIBIN    99.02207 1.8971410 15.36795 6.292509e-29 3.741468e-26 13.300779
PRRX2    80.18279 2.7710212 15.13155 1.981196e-28 1.126784e-25 13.734089
S1PR3    71.21109 3.7477246 15.02896 3.265870e-28 1.780035e-25 17.523437
CPED1   102.85334 2.0788448 14.92893 5.322870e-28 2.785138e-25 15.659027
CTHRC1   78.80884 4.8363794 14.81482 9.306949e-28 4.682469e-25 24.389212
POSTN   133.39569 3.8513366 14.58473 2.884441e-27 1.397458e-24 26.384484
HAND2   116.48710 2.7539369 14.31021 1.120933e-26 5.236760e-24 20.112630
EMP3     63.75094 5.6615425 14.15489 2.425144e-26 1.093907e-23 25.058909
TNNT2    85.05714 2.9350416 14.05066 4.076493e-26 1.777487e-23 15.103544
IFITM2   54.40575 5.5045974 13.99848 5.289394e-26 2.231953e-23 22.043856
ADGRA2   82.60776 2.0801881 13.93611 7.223507e-26 2.952834e-23  9.951716
PPIC     66.33688 5.7541758 13.77488 1.619989e-25 6.421539e-23 24.454184
PTH1R    81.86709 3.1660453 13.75780 1.764965e-25 6.610450e-23 15.399778
COL5A2   75.14705 5.1467724 13.75737 1.768716e-25 6.610450e-23 23.823467
HOXA13  102.49839 0.6432163 13.70643 2.284354e-25 8.300454e-23  7.279515
HGF     108.53089 1.0148773 13.61502 3.617731e-25 1.279015e-22  9.882073
TNNI1   108.76895 3.9575031 13.59767 3.947843e-25 1.358993e-22 22.393362
GPX8     42.24953 6.1566286 13.54314 5.196326e-25 1.742901e-22 22.636721
LGALS1   68.69366 6.8922090 13.36873 1.253724e-24 4.099990e-22 28.444800
ADAMTS1  68.57596 4.2288417 13.33013 1.524205e-24 4.862957e-22 17.479055
IGFBP4   55.21606 4.6457332 13.26680 2.100660e-24 6.542556e-22 16.569742
DACT3    62.13326 3.1881491 13.21989 2.664765e-24 8.106463e-22 10.934974
IL11RA   77.92492 3.4666733 12.83003 1.939196e-23 5.765142e-21 14.518390
PTGFR    85.70433 0.2592682 12.55070 8.105967e-23 2.356314e-20  3.534438
CCDC178  90.53569 0.8326892 12.52316 9.336784e-23 2.653371e-20  5.620593
GLT8D2   81.33065 2.0016704 12.51910 9.533555e-23 2.653371e-20  8.154654
DSC3     73.09694 1.9939554 12.27955 3.269119e-22 8.909031e-20  7.264299
EVA1B    58.75781 5.1275367 12.17275 5.670653e-22 1.513833e-19 17.438167
RGS5     84.95501 5.7892420 12.15141 6.331176e-22 1.656362e-19 23.063368

$`Intestinal epithelial cells`
             logFC   AveExpr        t      P.Value    adj.P.Val        B
APOB     129.95498 2.4186624 35.11027 7.644055e-61 9.999188e-57 41.87566
APOC1    102.22306 6.5875047 31.78707 1.359773e-56 7.316419e-53 65.66334
MTTP     140.38054 1.2912119 31.71861 1.677949e-56 7.316419e-53 35.35848
HNF4A    122.75461 1.2162260 29.80563 6.960383e-54 2.276219e-50 31.38704
APOA2    150.41088 4.5700960 28.44029 6.211640e-52 1.373633e-48 53.84341
FGB      149.49898 1.6909124 28.43604 6.300589e-52 1.373633e-48 37.71880
IHH      125.90842 1.5264822 28.36886 7.892873e-52 1.474952e-48 33.85802
AKR1D1   118.24768 0.8616420 27.08390 6.359570e-50 1.039869e-46 26.82426
LGALS2   113.24136 0.8459598 26.95531 9.951871e-50 1.446449e-46 25.97447
F2       108.45780 1.0658412 26.57627 3.760203e-49 4.918721e-46 26.36877
VIL1     102.87268 2.0194712 26.06824 2.283275e-48 2.644064e-45 30.54510
APOA1    185.01295 5.3603629 26.05134 2.425561e-48 2.644064e-45 58.09812
CCKBR    100.32241 2.8864382 25.98694 3.054535e-48 3.073568e-45 36.08047
DPP4     111.16138 2.0597924 25.71711 8.063341e-48 7.534040e-45 32.79172
SLC39A5  104.45023 0.8755279 25.68532 9.044632e-48 7.887522e-45 24.12762
S100A14  151.30196 2.3619882 25.49306 1.815480e-47 1.484268e-44 39.34440
S100A16  103.08890 4.6850373 25.40173 2.531051e-47 1.947569e-44 45.87603
PDZK1    110.63115 1.2293187 25.33917 3.179687e-47 2.310749e-44 27.16589
CST4     154.22922 1.5048488 25.26060 4.237002e-47 2.917064e-44 36.47398
FGFR1     51.99247 6.6221206 25.07050 8.508463e-47 5.564960e-44 51.75694
ADD3      51.98290 6.1224418 24.07269 3.518046e-45 2.191407e-42 46.15169
PCBD1     54.35431 6.9252945 23.74113 1.240833e-44 7.377881e-42 52.33702
SERPINE2 106.01883 6.3636276 23.70413 1.429277e-44 8.128860e-42 55.22374
FOXA2    124.88964 2.3626344 23.61529 2.008358e-44 1.094639e-41 35.11882
CYP4X1   100.75570 1.8636082 23.49951 3.132723e-44 1.639166e-41 28.00295
GSTA2    103.91056 1.8673218 23.46481 3.580188e-44 1.801247e-41 28.04614
HABP2    108.37819 0.6195381 23.28953 7.042669e-44 3.412043e-41 22.57591
APOM      88.30447 3.6040528 23.21230 9.499097e-44 4.437774e-41 35.28271
SMLR1     98.68692 1.1896931 23.00741 2.107725e-43 9.507293e-41 22.14613
FGFR4    102.71134 2.9248053 22.96574 2.480028e-43 1.081375e-40 33.57896
RBP4     111.19146 2.7061349 22.91325 3.044810e-43 1.284812e-40 33.88021
CST1     191.38537 3.0632741 22.57981 1.129310e-42 4.616407e-40 43.19309
FOXQ1    119.78729 2.0403927 22.34083 2.911995e-42 1.154297e-39 32.45299
PLA2G12B  94.11714 1.0113111 21.68918 3.986194e-41 1.533629e-38 19.79505
FZD4      71.45670 2.5833133 20.45452 6.510352e-39 2.433198e-36 23.67553
FGA      103.23256 1.1568505 19.97099 5.037309e-38 1.830362e-35 20.80888
CHDH      70.69916 2.5362295 19.87511 7.583689e-38 2.681142e-35 22.46718
GAMT      43.56159 6.5280758 19.82255 9.494932e-38 3.268506e-35 41.92461
SLCO2A1   88.65477 1.7276243 19.63253 2.146046e-37 7.198059e-35 22.61199
DENND2C   95.43203 2.2918567 19.31508 8.465243e-37 2.768346e-34 25.48421
MEP1A     89.49524 0.5183799 19.25852 1.082424e-36 3.453459e-34 14.75312
PPFIBP2   64.77025 3.1999294 19.06787 2.486330e-36 7.743734e-34 24.82958
MGST2     65.56294 5.7152198 18.77223 9.110286e-36 2.771434e-33 38.87630
ASGR2     84.90049 1.0898396 18.70249 1.239542e-35 3.685102e-33 17.09172
RAB25     90.46080 3.8125574 18.57204 2.208640e-35 6.420272e-33 31.70362
CTSE     110.34638 0.6346451 18.46498 3.553953e-35 1.010636e-32 18.24168
MARC1     54.65659 4.2794344 18.43570 4.048757e-35 1.126847e-32 28.41843
APOC3    108.78707 2.0026209 18.30954 7.108376e-35 1.937181e-32 24.61019
AMN      105.43030 1.7144345 18.26362 8.729249e-35 2.330353e-32 22.99892
CUBN      96.32447 1.3311249 18.06542 2.124577e-34 5.558319e-32 19.13330

$`Islet endocrine cells`
             logFC   AveExpr        t      P.Value    adj.P.Val         B
ADAMTS8  129.53805 1.5366492 26.43134 6.274147e-49 8.207212e-45 26.559205
SOST     174.42334 0.7495979 25.83500 5.271603e-48 3.447892e-44 30.636107
RIPPLY3  155.61377 2.0702438 22.83215 4.183273e-43 1.824047e-39 32.844015
SHC3     113.84060 1.3165005 22.66959 7.924827e-43 2.591616e-39 20.522624
SPARCL1  135.57671 1.4090763 22.50491 1.518573e-42 3.972891e-39 26.158014
NEFM     125.62682 3.9768428 20.09196 3.011091e-38 6.564681e-35 36.099754
ADAMTS3  105.98304 1.9854448 19.29360 9.293317e-37 1.736655e-33 19.982655
SOX2      92.95842 4.9189628 19.20445 1.369689e-36 2.239612e-33 35.061816
BMP7      65.02273 4.3748533 18.88442 5.558318e-36 8.078706e-33 26.715335
NEFL      94.09710 3.6652260 18.67045 1.428222e-35 1.868257e-32 27.924973
MUC12     82.88917 3.0025539 18.44101 3.954129e-35 4.702178e-32 21.033421
WNT1     126.77665 1.6014263 17.89197 4.646545e-34 5.065121e-31 22.254969
GDF7     128.75682 1.8171538 17.80884 6.769990e-34 6.812172e-31 23.068322
CTNNBIP1  39.15662 6.1871090 17.67897 1.221022e-33 1.140871e-30 30.833925
WNT3A    139.58409 1.2006581 17.26882 7.975502e-33 6.955170e-30 20.886580
LPL      121.11049 0.6072425 17.12012 1.583179e-32 1.294348e-29 12.929768
CBLN1    105.33229 1.2372319 16.96684 3.219255e-32 2.402381e-29 14.384192
IFIT1     88.55288 3.0191987 16.96112 3.305776e-32 2.402381e-29 20.893732
COL9A1   104.51779 2.4451146 16.24238 9.591145e-31 6.603251e-28 21.081582
LYPD1    107.78197 2.5433830 16.01103 2.874912e-30 1.880336e-27 20.834493
WNT10B    99.45440 0.8072800 15.82164 7.096417e-30 4.420392e-27 11.841066
ADGRV1    57.21112 4.3422610 15.67919 1.404254e-29 8.349569e-27 20.764235
PLEKHA5   40.69873 6.4797648 15.52835 2.900642e-29 1.649708e-26 28.721570
GAP43     75.31679 4.5145804 14.46015 5.334846e-27 2.907713e-24 23.238557
EPHA7     78.78219 3.9034653 14.43396 6.072705e-27 3.177482e-24 20.389815
TPBG     100.33057 6.1705964 14.31185 1.111856e-26 5.593916e-24 33.326828
ADCY2     95.13915 2.0573750 13.98630 5.620973e-26 2.723257e-23 11.846248
IL17RD    59.10545 3.5778488 13.90451 8.460777e-26 3.952694e-23 15.570387
UBE3D     48.01495 4.3941604 13.88658 9.255074e-26 4.060426e-23 17.585571
LMX1A    122.76479 1.1314147 13.88535 9.312192e-26 4.060426e-23 13.852762
IFITM2    52.20482 5.5045974 13.86883 1.011504e-25 4.268222e-23 22.663755
FAM181B  133.38352 3.4143865 13.54253 5.212215e-25 2.130656e-22 23.351210
SCG2      87.78095 0.7425984 13.36739 1.262241e-24 5.003447e-22  6.601143
PRCP      38.05816 5.5117030 13.35325 1.355849e-24 5.071740e-22 19.616674
CRYGS     83.79166 0.4106303 13.35308 1.357013e-24 5.071740e-22  5.603592
RBFOX1    88.75046 1.7136110 13.25294 2.253517e-24 8.188404e-22 11.716744
VAMP5     55.53149 3.9231323 13.20055 2.939515e-24 1.039238e-21 16.199904
CA10     100.98382 0.3247058 12.87761 1.520922e-23 5.235574e-21  4.861187
CDH18     99.62846 0.5513575 12.82950 1.944514e-23 6.522099e-21  7.814202
BCL2      84.60244 1.7992935 12.63277 5.320971e-23 1.740090e-20  9.677960
CD83      63.19196 2.6936773 12.62742 5.468993e-23 1.744875e-20  9.420532
IGFBP2    47.34541 8.9326234 12.49664 1.069877e-22 3.332157e-20 31.149551
FRMD3     79.98545 1.0067784 12.13875 6.758857e-22 2.056107e-19  5.380744
PCDH9     79.53995 2.6335691 12.05461 1.043919e-21 3.103525e-19 12.625904
PGAM2     59.64889 2.8311876 11.98572 1.490705e-21 4.333314e-19  9.933124
MMRN1    115.35697 1.7437715 11.96845 1.630118e-21 4.635559e-19 13.193607
MAFB      88.11635 2.8155107 11.87216 2.683885e-21 7.469767e-19 12.352118
HTRA1     68.46204 3.5987240 11.77574 4.424777e-21 1.205844e-18 13.169312
NMU       67.28790 3.1704973 11.62723 9.566725e-21 2.553925e-18 11.554305
SFRP2     59.78129 4.9878608 11.50988 1.761080e-20 4.607337e-18 17.723791

$MUC13_D
             logFC   AveExpr        t      P.Value    adj.P.Val         B
FAM184A  102.95228 3.7029690 20.60390 3.480193e-39 4.552440e-35 26.901403
APOA2    135.32537 4.5700960 20.28424 1.333858e-38 8.724098e-35 34.664384
FOXA2    129.82860 2.3626344 19.66000 1.906921e-37 8.314812e-34 23.070736
CST1     188.47474 3.0632741 19.00889 3.218806e-36 1.052630e-32 32.315029
CCKBR     96.54064 2.8864382 18.84157 6.711640e-36 1.755899e-32 19.794225
APOA1    160.12676 5.3603629 18.59859 1.963299e-35 4.280318e-32 38.895204
APOB     103.40119 2.4186624 18.47533 3.393978e-35 6.342374e-32 16.381441
PCBD1     55.40150 6.9252945 17.94765 3.612836e-34 5.907438e-31 31.924495
VIL1      98.62660 2.0194712 17.49520 2.823294e-33 4.103501e-30 13.119194
FOXQ1    122.03705 2.0403927 17.28702 7.334946e-33 9.594843e-30 18.133709
IHH      110.61487 1.5264822 16.92052 3.991566e-32 4.746698e-29 13.173958
EPSTI1    87.52356 3.4167152 16.88121 4.791867e-32 5.223534e-29 18.124665
PDZK1    102.13769 1.2293187 15.81284 7.401460e-30 7.447576e-27  9.554251
APOC1     73.31441 6.5875047 15.65024 1.613683e-29 1.507756e-26 28.446096
HNF4A    101.66672 1.2162260 15.57713 2.293456e-29 2.000046e-26  9.051511
PRSS2    145.60146 1.1202828 15.35733 6.624135e-29 5.415644e-26 17.077524
SERPINE2  91.48266 6.3636276 14.99486 3.857136e-28 2.967952e-25 28.554838
DENND2C  100.23173 2.2918567 14.84160 8.161992e-28 5.931501e-25 12.078375
CST4     129.04996 1.5048488 14.75038 1.276775e-27 8.790258e-25 14.445057
S100A16   83.99670 4.6850373 14.72340 1.457705e-27 9.308538e-25 20.151083
ADD3      45.34595 6.1224418 14.71834 1.494376e-27 9.308538e-25 20.703857
GATA4     90.72149 2.7684350 14.04010 4.297094e-26 2.555013e-23 13.336753
RAB25     90.26060 3.8125574 13.90390 8.486475e-26 4.826590e-23 16.426358
WFDC2     78.05954 5.5491577 13.85540 1.081916e-25 5.896892e-23 22.473366
SLC2A3    79.39011 6.2843433 13.74574 1.875111e-25 9.449104e-23 24.532227
RFX6      98.56307 0.4034583 13.74542 1.878119e-25 9.449104e-23  4.721693
KITLG     89.46728 2.8648700 13.72206 2.111827e-25 1.023141e-22 11.855039
SOX17    143.99145 2.5971138 13.64035 3.184667e-25 1.487808e-22 18.603259
ADM       85.49173 2.6525145 13.09889 4.926386e-24 2.222140e-21 10.550261
FGFR1     39.50602 6.6221206 12.93060 1.160630e-23 5.060735e-21 19.370426
FGFR4     84.70432 2.9248053 12.78172 2.482337e-23 1.047466e-20 10.940146
PRSS1    108.84084 0.8334319 12.26390 3.543666e-22 1.448584e-19  6.686932
CLDN3     73.98025 3.3835805 12.19927 4.945303e-22 1.960288e-19 10.350828
PRDM1     79.44786 2.2010891 12.06392 9.948370e-22 3.827489e-19  7.244811
MNX1      91.48632 1.5673352 12.02618 1.209190e-21 4.519260e-19  6.835304
GJA4      90.65862 1.4068779 11.97964 1.538366e-21 5.589825e-19  6.340237
FZD4      63.75631 2.5833133 11.90329 2.284222e-21 8.075649e-19  5.784391
S100A14  108.77660 2.3619882 11.86691 2.758027e-21 9.494144e-19 10.660375
CARHSP1   28.26924 7.6020921 11.85162 2.985385e-21 1.001329e-18 19.387196
DMKN      72.62431 6.0650201 11.79297 4.046430e-21 1.319979e-18 18.731492
HABP2     90.41071 0.6195381 11.78869 4.137233e-21 1.319979e-18  3.525355
PPFIBP2   58.77466 3.1999294 11.60090 1.096960e-20 3.416509e-18  7.014022
HHEX      96.14615 1.3410679 11.53735 1.526515e-20 4.587493e-18  7.294957
MGST2     56.24558 5.7152198 11.53528 1.543075e-20 4.587493e-18 15.792397
CST2      81.87065 0.8339147 11.42718 2.708386e-20 7.872976e-18  2.553418
EPCAM     95.64573 5.6005879 11.14023 1.209130e-19 3.438397e-17 17.882056
GASK1B    85.20493 1.9409450 11.02529 2.203712e-19 6.075745e-17  5.790553
LGR5      83.05251 2.0058344 11.02307 2.229461e-19 6.075745e-17  6.808390
TTN       75.05294 3.0232797 10.64108 1.644022e-18 4.388868e-16  7.549533
PLCXD3    74.53492 1.3469952 10.60624 1.973010e-18 5.161790e-16  2.526662

$`Mesangial cells`
             logFC   AveExpr         t      P.Value    adj.P.Val         B
TWIST1   116.82967 3.0945849 20.327052 1.113387e-38 1.456421e-34 29.730429
PRRX2     87.08075 2.7710212 18.058779 2.189079e-34 1.055745e-30 18.963311
COL6A3   116.00242 3.4290288 18.036393 2.421249e-34 1.055745e-30 28.313147
NID2      96.51343 3.8234636 16.723149 1.000967e-31 3.273412e-28 25.539942
HOXA13   109.45805 0.6432163 16.548997 2.261975e-31 5.917780e-28 11.857422
HOXA10   126.28667 0.7580840 16.500750 2.837080e-31 6.185308e-28 15.101555
ALX4     111.28615 1.0738475 16.073890 2.132089e-30 3.984265e-27 13.211826
PCOLCE    81.86994 4.8474419 15.829942 6.820231e-30 1.115193e-26 26.914598
DDR2      91.63365 2.8971187 15.330128 7.556432e-29 1.098285e-25 18.098237
EMILIN1   84.22150 2.8739884 14.479724 4.843022e-27 6.335157e-24 15.721708
BMP4      71.13083 4.6916506 13.978853 5.834093e-26 6.937798e-23 21.124887
CYB5A     55.89047 8.2444517 13.840114 1.168016e-25 1.273235e-22 32.965387
HOXA11   102.76464 0.3264158 13.206520 2.851773e-24 2.869542e-21  6.587248
PRRX1    146.73885 2.8898239 13.111484 4.620935e-24 4.317604e-21 21.687755
COL6A2    68.97292 6.2693029 12.959083 1.003759e-23 8.753445e-21 25.538797
DACT3     59.06204 3.1881491 12.591909 6.561173e-23 5.364169e-20 10.292378
VEGFC     88.91695 2.6180935 12.574949 7.157522e-23 5.507503e-20 12.824584
HOXC9     99.58343 1.0531477 12.412520 1.648615e-22 1.198085e-19  8.084623
COL1A1    79.41989 6.2764999 12.024132 1.222096e-21 8.413809e-19 23.289497
COL3A1   115.91428 5.3883411 11.874927 2.645739e-21 1.730446e-18 22.488557
HAND2    102.03943 2.7539369 11.663957 7.904901e-21 4.924000e-18 14.049291
CYB5D1    55.54760 3.8300429 11.558147 1.370037e-20 8.146117e-18 11.240163
HPSE2     80.38155 1.2954474 11.536848 1.530526e-20 8.704700e-18  5.091416
WNT5A     80.37717 3.8710975 11.515957 1.706234e-20 9.299688e-18 15.235404
ADGRA2    72.36707 2.0801881 11.506360 1.793587e-20 9.384765e-18  6.585727
S1PR3     57.49998 3.7477246 11.365801 3.728733e-20 1.875983e-17 11.074215
PCDH18    55.93164 3.4732442 11.296145 5.360730e-20 2.597174e-17  9.284439
EPB41L2   33.95835 5.7366211 11.267859 6.212652e-20 2.902418e-17 15.032487
TNS1      78.35510 1.7631603 11.207840 8.496460e-20 3.832489e-17  6.246833
KYNU      79.89166 3.0419096 11.047416 1.963194e-19 8.560180e-17 11.363501
PITX1    103.02338 4.7599224 10.991320 2.631765e-19 1.110520e-16 18.453138
COL6A1    50.05993 6.8556861 10.941577 3.413143e-19 1.395229e-16 20.459512
SERTAD4   73.45759 2.2408554 10.919701 3.826676e-19 1.516871e-16  6.919804
HOXA9    106.60821 0.5038266 10.858596 5.267254e-19 2.026498e-16  5.286805
AURKB     41.70904 5.1786100 10.738625 9.866509e-19 3.687537e-16 12.997355
KCTD12    67.44376 3.9630040 10.617705 1.858011e-18 6.751289e-16 12.109025
TBX4      78.05631 0.2957617 10.418447 5.275571e-18 1.865128e-15  1.727350
CDK6      33.91371 6.0423700 10.378490 6.504003e-18 2.238917e-15 14.668007
RARG      62.19693 2.4628392 10.179215 1.847719e-17 6.197439e-15  5.078000
SGCG      79.07164 1.1544379 10.011852 4.440856e-17 1.420810e-14  3.590516
LUM       96.09118 4.7155844 10.011319 4.453267e-17 1.420810e-14 14.972496
CTHRC1    58.06550 4.8363794  9.770576 1.571293e-16 4.893831e-14 11.947455
PGM5      82.36090 2.3608095  9.567169 4.555026e-16 1.385681e-13  7.097047
FGF20     70.04667 0.7507092  9.543386 5.158235e-16 1.533520e-13  1.245595
IGFBP4    42.33632 4.6457332  9.471204 7.522619e-16 2.151136e-13  8.809172
FREM1     71.12520 3.3016262  9.470140 7.564578e-16 2.151136e-13  8.061379
CLMP      46.65113 4.1086201  9.449748 8.415144e-16 2.342096e-13  7.893993
MIS18BP1  32.87955 5.9977414  9.412570 1.021921e-15 2.784948e-13 11.768946
IFITM2    39.45785 5.5045974  9.312745 1.721003e-15 4.594374e-13 10.822409
BAMBI     50.79116 6.5277939  9.065383 6.247927e-15 1.634583e-12 13.691003

$`Mesothelial cells`
             logFC   AveExpr        t      P.Value    adj.P.Val        B
SLC9A3R1  95.26541 6.6814823 38.25505 1.451018e-64 1.898076e-60 65.05152
COBLL1   109.78213 3.8078148 33.33068 1.305731e-58 8.540135e-55 43.41512
CARD16   146.36601 0.4869025 31.76006 1.477300e-56 6.441521e-53 28.79722
KRT24    151.96765 0.6689462 31.46143 3.708873e-56 1.212894e-52 30.99165
AQP1     154.68372 1.8756794 31.00990 1.511991e-55 3.955671e-52 38.02760
CD44     120.80047 2.5102088 28.87492 1.460627e-52 3.184411e-49 33.87043
FIBIN    128.17481 1.8971410 26.70966 2.351515e-49 4.394310e-46 31.21844
SLC5A12  131.74269 2.7850221 26.48915 5.113882e-49 8.361837e-46 37.10488
ANXA8    129.20971 0.8855355 25.29954 3.674710e-47 5.340987e-44 24.43782
OLR1     126.36372 0.3537423 25.02507 1.005671e-46 1.262638e-43 21.00239
SLC34A2  136.42294 0.5276665 25.01033 1.061771e-46 1.262638e-43 22.95760
TGFBR3    95.88568 3.1869881 24.19296 2.233670e-45 2.434886e-42 30.92889
SLC40A1  120.12887 3.3828801 23.96816 5.227803e-45 5.260376e-42 37.18121
MYL4     122.65111 3.2151048 22.34731 2.837965e-42 2.600522e-39 35.35263
LIMS1     49.31521 6.2651233 22.33356 2.997472e-42 2.600522e-39 40.64753
SVEP1     95.05711 2.2052858 22.31864 3.180823e-42 2.600522e-39 23.30076
ZNF641    79.94426 3.6994094 22.02784 1.016975e-41 7.825324e-39 29.69126
FRZB     131.01694 5.4381793 21.83736 2.189120e-41 1.590882e-38 47.07973
STX18     56.55477 5.5193489 21.75925 3.001450e-41 2.066419e-38 36.91805
SLC7A7   111.20631 2.5859236 21.65570 4.565913e-41 2.986336e-38 28.34319
AKAP12    80.88309 6.6390237 21.54339 7.207201e-41 4.489400e-38 47.19852
TNNT2    106.04261 2.9350416 21.33505 1.687352e-40 1.003284e-37 28.92080
TNFAIP3   87.61491 2.5601386 20.91428 9.554422e-40 5.433974e-37 22.41627
MORC4     65.81007 3.6446214 20.30462 1.223879e-38 6.670649e-36 23.84649
LEPROTL1  48.44800 6.6570553 20.04930 3.609392e-38 1.888578e-35 40.55297
GALNT10   76.85768 3.8606737 19.91599 6.368937e-38 3.204310e-35 27.99135
HSBP1L1   84.18495 3.4655492 19.86024 8.081426e-38 3.915301e-35 26.74346
DSC3      92.32285 1.9939554 19.74340 1.332818e-37 6.226640e-35 19.16457
INMT     101.81189 1.6400162 19.70742 1.555401e-37 7.015932e-35 19.09948
BCO2      90.42834 1.8742312 19.66186 1.891688e-37 8.248390e-35 17.58932
LUM      151.95763 4.7155844 19.28882 9.488361e-37 4.003782e-34 39.75903
SARAF     39.25828 7.8538281 19.12121 1.969320e-36 8.050211e-34 43.35662
JDP2      78.92256 3.6520054 19.00015 3.344447e-36 1.325719e-33 25.88144
AKR1B15  105.39495 1.5067348 18.97344 3.759846e-36 1.446546e-33 18.79866
SLN      155.68544 2.2626310 18.95779 4.027021e-36 1.505070e-33 31.23188
BNC1     104.24701 1.2420685 18.86958 5.933282e-36 2.155924e-33 17.03703
CREB3L1   90.56099 3.4812380 18.75946 9.638359e-36 3.407551e-33 26.57437
MYRF      82.88034 3.1829695 18.69162 1.300565e-35 4.393067e-33 23.04060
PXK       62.40135 3.8629424 18.69003 1.309759e-35 4.393067e-33 23.32941
IL6R     106.75300 1.5036185 18.50647 2.955136e-35 9.664033e-33 18.07065
IFIT1     92.14588 3.0191987 18.33682 6.292818e-35 2.007716e-32 23.55696
POSTN    151.33344 3.8513366 17.92884 3.933230e-34 1.225014e-31 35.00866
LRRC1     63.28836 3.6485961 17.80459 6.901817e-34 2.099597e-31 20.63788
PRSS35    98.66016 3.2397555 17.75745 8.547369e-34 2.541094e-31 25.68415
CTHRC1    85.76302 4.8363794 17.73235 9.579367e-34 2.784616e-31 32.22821
BNC2      88.35269 3.2479340 17.69253 1.147984e-33 3.264517e-31 23.68829
EGFL6    140.13891 1.8276028 17.60414 1.716882e-33 4.778412e-31 25.63787
CEBPD     91.70653 3.4107596 17.55290 2.168983e-33 5.910931e-31 25.24229
RAMP1     94.49397 3.0053905 17.52437 2.470928e-33 6.596369e-31 23.08838
DOK4      62.42553 4.8213956 17.48477 2.961329e-33 7.747429e-31 27.65548

$`Metanephric cells`
           logFC     AveExpr         t      P.Value    adj.P.Val           B
HOXA7  158.80141  0.44560566 22.646239 8.688901e-43 1.136595e-38 17.42554165
HOXC9  131.30059  1.05314774 17.175568 1.225620e-32 8.016166e-29 12.98481379
CDX4   136.49107  0.69810211 16.855800 5.393079e-32 2.351562e-28 11.61422218
HOXA10 133.08989  0.75808397 15.029802 3.252435e-28 1.063627e-24 10.35270820
HOXB9  157.29160  1.08866162 14.941865 4.996794e-28 1.275133e-24 15.05141625
HOXA9  139.03838  0.50382655 14.909669 5.848786e-28 1.275133e-24  9.65440425
HOXC6  130.90841  1.62292046 14.545690 3.496750e-27 6.534428e-24 13.02237384
URAD   117.96737  2.26636107 13.645606 3.101572e-25 5.071458e-22 12.66014129
HOXC8  126.24909  2.24639430 13.247679 2.314458e-24 3.363936e-21 13.43328172
HOXD9  102.76651  0.02191740 11.622086 9.825986e-21 1.285337e-17  2.22971641
HOXC4   99.01172  0.84916411 11.479458 2.063102e-20 2.453404e-17  2.89404325
HOXA5  108.66865  0.12434508 11.415118 2.883996e-20 3.143796e-17  2.44506955
HOXD4  107.02448 -0.10837864 11.295956 5.366031e-20 5.399465e-17  1.88351349
HOXC10 104.20590  0.34494651 11.158986 1.096366e-19 1.024398e-16  2.17504194
HES7    98.10440  0.61844914 10.554803 2.582814e-18 2.252386e-15  1.44466878
HOXD3  101.21432 -0.05480809  9.916242 7.327894e-17 5.991011e-14  0.28702066
HOXA6   92.09069 -0.13074454  9.756541 1.691086e-16 1.301241e-13 -0.07701277
WNT5A   80.79595  3.87109754  9.359924 1.345311e-15 9.776677e-13  7.58732351
FZD10   92.66475  1.64816950  9.244160 2.461415e-15 1.694620e-12  2.27484052
CDX2   110.22885  3.39599403  9.193238 3.209945e-15 2.099464e-12  8.13425440
SALL1   66.83448  3.52940145  9.149307 4.035774e-15 2.513903e-12  4.55843812
FGF8    90.74090  2.27163976  8.844193 1.972431e-14 1.172790e-11  3.22511693
BMP4    60.29008  4.69165060  8.450799 1.508590e-13 8.374926e-11  5.22620368
HOXB3   93.07565  2.81409534  8.447232 1.536566e-13 8.374926e-11  4.31763909
FOXF2   79.38915  1.72055207  8.300967 3.260538e-13 1.706044e-10  1.15642660
FOXB1   81.75363  1.17327676  8.243733 4.373682e-13 2.200467e-10 -0.64773876
HOXD8   87.23346 -0.07212554  8.108583 8.736540e-13 4.232692e-10 -1.28104130
MLLT3   62.22285  5.07183549  7.963603 1.830183e-12 8.550221e-10  5.77002038
RARG    64.28507  2.46283917  7.851474 3.235643e-12 1.459498e-09 -0.13842061
PRRX2   61.17551  2.77102125  7.825529 3.690618e-12 1.609232e-09  0.51598081
HOXA3  108.15130  0.54333794  7.804023 4.115547e-12 1.736628e-09  0.41333637
FGF17  120.97491  2.12486885  7.754855 5.278511e-12 2.157756e-09  3.99247093
HOXB8   99.36657  2.17965111  7.725072 6.136143e-12 2.432330e-09  2.54130507
MCM7    34.39258  6.55663259  7.606184 1.117501e-11 4.299419e-09  5.78407068
HOXB7   84.81812  2.06936902  7.506908 1.839972e-11 6.876763e-09  0.84533700
GTF3A   23.25751  7.08828325  7.446532 2.489581e-11 9.046168e-09  5.86878932
MCM3    28.34464  6.37609094  7.371435 3.622700e-11 1.280771e-08  4.57232979
PRRX1  118.25370  2.88982390  7.323080 4.609643e-11 1.586809e-08  3.96796613
NASP    23.94041  8.81893924  7.309735 4.926142e-11 1.652278e-08  8.33787422
MCM4    33.76286  5.61462224  7.290575 5.418615e-11 1.772023e-08  3.22453738
TGFBI   74.10172  3.29600219  7.169415 9.880399e-11 3.152329e-08  1.23164197
HNRNPD  16.04178  8.77013265  7.082118 1.520129e-10 4.734477e-08  7.15132276
HOXA4   77.91954 -0.04234780  7.051897 1.763923e-10 5.366018e-08 -2.03819855
HOXA11  80.77753  0.32641585  6.971940 2.611820e-10 7.764823e-08 -1.81744140
SKAP2   60.37785  1.98994353  6.955780 2.826936e-10 8.217590e-08 -1.14420591
NID2    63.93392  3.82346364  6.920700 3.356095e-10 9.543713e-08  1.66037591
CENPF   46.35478  8.07651079  6.770823 6.961661e-10 1.937564e-07  6.90678004
SALL4   41.47067  5.74912108  6.729399 8.508477e-10 2.318737e-07  3.22378683
MSGN1   91.22716  0.43441408  6.675921 1.101673e-09 2.941016e-07 -1.80709977
DEK     21.03932  8.03922184  6.650019 1.248178e-09 3.265484e-07  5.20493264

$`Retinal pigment cells`
               logFC     AveExpr         t      P.Value    adj.P.Val         B
SFRP2      141.32830  4.98786079  36.33907 2.492096e-62 3.259911e-58 58.246252
DCT        183.61646  0.92656067  26.51734 4.629126e-49 2.303410e-45 32.776867
CCL2       136.54778  2.53603706  26.47996 5.282647e-49 2.303410e-45 34.919564
RAX        155.02632  0.81413097  26.00803 2.832239e-48 9.262130e-45 27.200686
DAPL1      169.08091  0.64783606  24.57243 5.382477e-46 1.408164e-42 28.013147
SIX6       163.56354  0.85100235  22.86087 3.737934e-43 8.149318e-40 26.992171
MITF       108.93119  2.41605164  22.72373 6.403785e-43 1.196684e-39 26.329393
CLEC19A    119.34980  0.36711015  21.81131 2.431918e-41 3.976489e-38 16.678809
HOMER2      86.08452  2.81496580  21.50547 8.410835e-41 1.222468e-37 23.523422
ALDH1A1    142.61414  2.18517354  19.87570 7.564462e-38 9.895072e-35 28.225173
PMEL       139.53463  4.87775775  19.32253 8.195613e-37 9.746074e-34 41.143281
CCKBR       89.26744  2.88643816  18.87949 5.680199e-36 6.191890e-33 22.492708
DBX2       112.03552 -0.01289448  18.29197 7.689521e-35 7.737433e-32 10.700173
PGAM2       74.09051  2.83118756  16.26100 8.782972e-31 8.206433e-28 16.640217
AL391650.1 109.10959  1.17877935  15.64053 1.690746e-29 1.474443e-26 14.816826
SYNPR       97.70663  0.48089549  14.93305 5.216913e-28 4.265152e-25  8.737079
MAB21L1    102.73132  1.23913399  14.66734 1.920325e-27 1.477634e-24 12.139598
TRPM3      102.55519  2.49547548  14.46031 5.330624e-27 3.873883e-24 18.196964
SIX3       122.14977  2.60080335  14.16696 2.283704e-26 1.572270e-23 19.577923
RAB27A      65.41879  2.73489754  14.13558 2.669800e-26 1.746182e-23 10.697499
TYR         95.96543 -0.08943723  13.97099 6.067934e-26 3.779745e-23  6.701123
TYRP1      106.50732  1.41698662  13.34262 1.430773e-24 8.290311e-22 12.718529
SERPINF1    78.13441  5.73659766  13.33726 1.470131e-24 8.290311e-22 25.846696
SOX2        72.25486  4.91896284  13.33054 1.521042e-24 8.290311e-22 21.653396
PLCH1       66.94320  2.87856906  13.31750 1.624793e-24 8.501565e-22 12.749677
ATP6V1C2    96.37624  1.19716966  13.26123 2.160806e-24 1.087135e-21 11.980023
SPOCK1      76.22616  3.06394163  12.77136 2.617349e-23 1.268057e-20 13.681686
BMP7        50.76819  4.37485330  12.72694 3.285079e-23 1.534718e-20 14.596731
DIPK1C     113.66888  0.46823211  12.30052 2.934204e-22 1.303677e-19  8.728931
CRABP1     106.65448  6.11607830  12.29688 2.989856e-22 1.303677e-19 26.831918
MYO3B       73.90201  1.03301423  12.15827 6.110711e-22 2.578523e-19  5.766586
SFRP1       66.19226  6.27492262  12.11178 7.769063e-22 3.175847e-19 23.253401
HCRT        81.20656  0.64094386  12.00438 1.353542e-21 5.365360e-19  5.743734
EFNA5       72.22309  5.18781468  11.91943 2.100975e-21 8.083192e-19 19.952141
CLDN1       72.68037  1.53908082  11.82592 3.410856e-21 1.274783e-18  7.727196
ANXA1      115.38067  3.63810634  11.65727 8.184363e-21 2.973879e-18 17.782423
CRX         83.21879  0.28441292  11.52890 1.595107e-20 5.639350e-18  3.700153
SNCA        55.07566  4.74965867  11.49838 1.869634e-20 6.391661e-18 15.564666
TSPAN10     69.65780  2.46668310  11.49472 1.905625e-20 6.391661e-18  9.926649
LAMP5       83.57894  0.69345385  11.43581 2.589448e-20 8.468141e-18  3.786323
MAB21L2     78.80199  2.77646879  11.41038 2.956109e-20 9.431429e-18 11.288639
EFEMP1      68.29351  2.13398293  11.37250 3.600804e-20 1.121479e-17  6.770419
STRIP2      61.82783  1.70241747  11.15073 1.144671e-19 3.482196e-17  5.255785
ALDH1A3    104.69322  1.01266988  10.94704 3.317025e-19 9.861364e-17  6.784592
TRPM1       76.92175 -0.26571923  10.90268 4.182929e-19 1.215931e-16  2.578834
PAX6       111.96694  3.52118809  10.86096 5.202587e-19 1.479458e-16 15.750825
TCEAL7      68.18248  4.22573100  10.83887 5.839717e-19 1.600459e-16 13.246197
S100A11    -63.50749 10.01712682 -10.83779 5.872795e-19 1.600459e-16 16.263682
PTPRZ1      73.73152  3.76794437  10.82928 6.140223e-19 1.639189e-16 12.713017
SEMA3A      53.66653  4.37055799  10.81793 6.515743e-19 1.704649e-16 12.831813

$`SLC24A4_PEX5L positive cells`
            logFC   AveExpr        t      P.Value    adj.P.Val        B
GNG3    152.37451 2.6673015 45.39624 4.087886e-72 5.347364e-68 40.71307
INA     149.62034 2.6686304 40.07271 1.346128e-66 8.804353e-63 39.55716
STMN4   182.63416 1.8398121 36.62746 1.131932e-62 4.935601e-59 39.56391
TUBB2B   90.03668 8.1127821 34.86748 1.521483e-60 4.975630e-57 67.76138
TMEM163 148.20156 1.1117885 33.73003 4.040031e-59 1.056953e-55 26.56300
SLC17A6 156.20164 0.7775274 33.60118 5.891399e-59 1.284423e-55 26.52526
RTN1    162.71114 3.1365014 32.33098 2.591724e-57 4.843192e-54 42.78340
CRMP1   131.18170 3.7555245 32.15584 4.408636e-57 7.208671e-54 40.43336
NSG2    159.14008 0.4217989 31.09659 1.152982e-55 1.675795e-52 24.35030
KIF5C   125.61170 4.4306399 30.62587 5.060995e-55 6.620287e-52 43.83786
CDKN2D  100.41004 3.4783630 30.55754 6.282688e-55 7.471258e-52 30.94207
GAP43   136.48913 4.5145804 30.50016 7.535670e-55 8.214509e-52 46.45598
PCSK1N  136.60869 3.7471102 30.16376 2.200818e-54 2.214530e-51 40.56394
DCX     148.85898 2.6276693 30.10285 2.674899e-54 2.499311e-51 36.24807
OLFM1   132.03483 2.7883832 29.71992 9.183655e-54 8.008759e-51 33.78192
TLCD3B  140.62775 1.7731339 29.65057 1.149783e-53 9.400194e-51 27.47940
ELAVL3  145.53091 2.1343713 29.51288 1.798541e-53 1.383925e-50 31.67273
TTC9B   154.83111 0.4408217 29.32343 3.337560e-53 2.425479e-50 22.03152
CELF3   141.56814 1.2546600 29.18507 5.252814e-53 3.616425e-50 24.98545
UNCX    150.78647 0.8871815 28.60949 3.528499e-52 2.307815e-49 24.08694
SYP     137.22088 1.8687858 27.96024 3.134645e-51 1.952585e-48 27.29609
LHX9    151.27418 2.0780892 27.66748 8.499853e-51 4.886776e-48 31.62018
STMN2   170.33950 4.7054494 27.66432 8.592299e-51 4.886776e-48 53.31682
MAP1B    87.32345 8.7464887 26.84085 1.484573e-49 8.091542e-47 64.42512
MAB21L1 152.69616 1.2391340 26.68745 2.542387e-49 1.330279e-46 26.26312
MLLT11   90.24958 7.5497265 26.37986 7.529071e-49 3.787991e-46 56.64743
KLC1     56.92669 5.7901257 26.32269 9.221996e-49 4.467886e-46 35.60447
MYT1L   141.83040 0.4248931 25.28321 3.900742e-47 1.822343e-44 18.13178
PCSK2   138.60491 1.2535270 25.22275 4.866509e-47 2.195131e-44 22.25312
ADCYAP1 133.25161 0.8113424 25.18616 5.564609e-47 2.426355e-44 18.90266
CDK5R2  121.62164 0.4570845 23.88474 7.177352e-45 3.028611e-42 12.69251
INSM1   119.44623 1.9175950 23.70350 1.432730e-44 5.856731e-42 21.67223
GNAO1   113.22976 1.3581541 23.66724 1.645894e-44 6.524224e-42 16.49048
SNAP25  113.30137 1.6462144 22.67535 7.747204e-43 2.980623e-40 18.00343
GDAP1L1 139.72309 1.4553746 22.40688 2.239788e-42 8.371048e-40 22.51823
POU2F2  105.77498 2.4044080 22.25935 4.028113e-42 1.463660e-39 19.76063
NEFL    113.34640 3.6652260 22.08429 8.109424e-42 2.867010e-39 30.55475
GDAP1    82.54007 3.3711802 21.93249 1.491913e-41 5.135713e-39 20.72740
TAGLN3  140.61725 3.8492674 21.78076 2.751485e-41 9.152310e-39 36.41540
PRPH    122.85085 2.2754711 21.77655 2.798658e-41 9.152310e-39 24.64320
NRXN1   122.97923 2.7210766 21.62150 5.245896e-41 1.673697e-38 26.01677
NDRG4   103.59407 2.6253264 21.57340 6.378749e-41 1.986677e-38 20.28409
NSG1    100.33655 4.1692336 21.35639 1.546149e-40 4.703529e-38 30.21726
NHLH2   109.85331 1.9647414 21.23824 2.509788e-40 7.461485e-38 18.42603
ELAVL2  114.95598 2.7520644 21.18410 3.135266e-40 9.113869e-38 24.59542
SCN3B   111.49643 0.9519570 21.10589 4.326750e-40 1.230396e-37 12.47056
TUBA1A   93.41180 9.5832524 21.08310 4.753234e-40 1.322916e-37 59.67462
SYT1    108.41512 4.4850794 20.96972 7.593853e-40 2.067499e-37 33.90290
KLHL35  118.94251 2.1556421 20.96497 7.744625e-40 2.067499e-37 21.19815
ACTL6B  127.67692 0.6081244 20.83884 1.306778e-39 3.418793e-37 13.89705

$`Squamous epithelial cells`
             logFC     AveExpr        t      P.Value    adj.P.Val         B
KRT7     176.08989  0.74277684 33.07127 2.815132e-58 3.682474e-54 31.589294
TACSTD2  179.76022  1.12840782 31.91331 9.236358e-57 6.041040e-53 33.530498
SFN      157.47289  1.34530658 30.16803 2.170976e-54 9.466179e-51 30.077340
TINCR    142.00712  1.03798232 30.07518 2.923049e-54 9.559102e-51 23.745486
NECTIN4  142.03122  0.56824527 29.51662 1.776755e-53 4.648347e-50 22.712738
WNT6     173.59437  0.50925547 26.86826 1.348842e-49 2.940700e-46 28.032573
GABRP    160.32536  0.57486256 25.92246 3.849477e-48 7.193573e-45 24.999699
ITGB6    142.93595  0.23176538 25.69836 8.628281e-48 1.410832e-44 18.071851
CLDN4    155.16655  2.92753410 25.64577 1.043533e-47 1.516717e-44 36.564768
LYPD3    143.36843  0.70675295 25.55490 1.450368e-47 1.897227e-44 21.474028
VGLL1    144.69168  0.09355883 25.30054 3.661278e-47 4.353925e-44 17.880676
VTCN1    158.83857  0.34406005 25.17310 5.837468e-47 6.363326e-44 23.370408
TMEM40   135.77703  0.15551975 23.65300 1.738156e-44 1.748986e-41 14.330060
MUC15    139.28388  0.11722375 23.47131 3.491804e-44 3.262592e-41 18.141643
GPRC5A   141.22647  0.40084966 22.01680 1.063067e-41 9.270649e-39 15.657218
TMEM54    90.53047  3.58307930 21.72509 3.446451e-41 2.817689e-38 26.030953
EPAS1    108.40412  2.45353489 21.68355 4.078285e-41 3.138121e-38 22.968469
RAB25    113.42922  3.81255735 21.27318 2.174404e-40 1.580187e-37 31.255957
S100A16  101.93139  4.68503728 21.00140 6.661194e-40 4.586056e-37 33.485563
TPM1      68.62426  8.87944070 20.16687 2.191434e-38 1.433308e-35 51.013640
S100A11   63.49027 10.01712682 20.10143 2.892381e-38 1.801678e-35 54.961971
KRT18     89.25220  8.52937448 19.87674 7.531061e-38 4.477901e-35 48.951743
PRKCH     98.71404  0.99175495 19.68470 1.714830e-37 9.752910e-35  9.983866
ERP27    114.33751  1.31781648 19.58426 2.641856e-37 1.439922e-34 15.983466
TRIM55   115.43699  0.37550628 19.42297 5.302435e-37 2.774446e-34 11.000128
KRT8      74.31422  8.88754755 19.12174 1.964722e-36 9.884821e-34 48.493521
RHOV     116.14032  1.20764426 18.89953 5.201112e-36 2.519843e-33 14.384246
ZNF750   118.74542  0.08346852 18.84414 6.636192e-36 3.100287e-33 10.701398
CLIC3    128.43552  1.68014670 18.64663 1.586965e-35 7.158307e-33 19.417281
EPN3     111.69865  0.39052705 18.59390 2.004574e-35 8.740610e-33  9.382514
XAGE2    135.31802  0.25657422 18.54110 2.533748e-35 1.069160e-32 12.621753
SPNS2     99.70094  0.89107234 18.34662 6.023484e-35 2.443028e-32 10.692497
CST6     151.47402  0.76838894 18.34148 6.163131e-35 2.443028e-32 17.720707
SMAGP     76.67694  3.49492966 18.28699 7.862563e-35 3.025005e-32 19.538724
KRT19     76.57681  8.67978966 18.23837 9.773872e-35 3.652915e-32 44.790067
ELF3      97.77304  3.23883569 17.99717 2.889365e-34 1.049883e-31 22.047183
ANXA3    102.86632  4.34168451 17.92027 4.088549e-34 1.445468e-31 28.149456
TINAGL1  120.46821  0.81955876 17.75960 8.464448e-34 2.913775e-31 12.610202
CYP1A1   116.64446  0.68297805 17.73517 9.457487e-34 3.172138e-31 12.444150
P2RY6    114.57426  1.22280370 17.70320 1.093624e-33 3.576423e-31 13.385563
ST14     116.28871  1.53593571 17.62176 1.584406e-33 4.994180e-31 14.925605
PLAU     106.13067  1.91522027 17.61913 1.603513e-33 4.994180e-31 16.203624
S100A9   168.44350  0.31810941 17.53447 2.359535e-33 7.177925e-31 18.927392
ANXA1    157.48290  3.63810634 17.50373 2.715334e-33 8.072564e-31 31.249388
TACC1     74.97340  3.71678785 17.37375 4.924529e-33 1.431506e-30 19.419911
CLDN3     88.72676  3.38358047 17.36078 5.226465e-33 1.486247e-30 20.401627
ELF5     112.43417 -0.11482346 17.22766 9.639814e-33 2.682945e-30  7.927264
ARHGAP29  70.19983  5.06595765 17.19085 1.142208e-32 3.112755e-30 26.422630
EGFR      82.92879  2.11760612 17.08140 1.893568e-32 5.055053e-30 11.263889
PTGES    111.41585  1.41220432 16.91180 4.156591e-32 1.087447e-29 13.512721

$`Stellate cells`
             logFC   AveExpr        t      P.Value    adj.P.Val        B
ANGPTL6  125.67056 1.2356458 30.14263 2.354817e-54 3.080337e-50 27.81265
SLC9A3R1  69.49483 6.6814823 25.39139 2.628241e-47 1.719001e-43 50.05698
COLEC10  120.01790 0.3153389 24.14257 2.701383e-45 1.177893e-41 17.89767
TGFBR3    94.40351 3.1869881 24.06400 3.635654e-45 1.188950e-41 31.28339
COLEC11  115.33599 1.6066477 23.88001 7.307783e-45 1.911862e-41 24.73567
FIBIN    117.75717 1.8971410 23.60887 2.058413e-44 4.487684e-41 27.82765
COBLL1    82.41871 3.8078148 22.42258 2.104447e-42 3.932609e-39 31.65674
SVEP1     90.95072 2.2052858 20.95363 8.117182e-40 1.194500e-36 21.77151
CPED1    119.99761 2.0788448 20.95063 8.218408e-40 1.194500e-36 27.41142
TSLP     123.91560 1.6183551 20.77620 1.695613e-39 2.218032e-36 25.15464
LUM      157.93497 4.7155844 20.50950 5.168471e-39 6.146252e-36 42.56861
DOK4      68.59864 4.8213956 20.20463 1.867550e-38 2.035785e-35 32.86736
FOXF1    108.38694 1.7924233 19.97535 4.944579e-38 4.975388e-35 22.61515
KCNE4    109.04846 0.5312068 19.83291 9.083128e-38 8.486885e-35 14.64908
COL1A1   111.23057 6.2764999 19.60776 2.387555e-37 2.082107e-34 44.72722
TEK      112.48944 1.4671969 19.34306 7.496899e-37 6.129184e-34 20.67891
JDP2      77.32241 3.6520054 18.75651 9.764376e-36 7.513400e-33 25.90236
ADGRA2    91.19337 2.0801881 18.68495 1.339494e-35 9.734399e-33 18.91592
CYB5D1    72.78877 3.8300429 18.60988 1.867475e-35 1.285707e-32 25.77001
CTHRC1    87.92594 4.8363794 18.44805 3.832214e-35 2.506459e-32 33.83901
ZNF641    70.05060 3.6994094 18.39708 4.809054e-35 2.995583e-32 24.57582
AKAP12    70.79968 6.6390237 18.23995 9.704788e-35 5.770379e-32 40.24017
LDB2      91.42219 3.3761267 18.13909 1.525621e-34 8.676803e-32 25.84461
IGF2     136.40483 3.4009741 18.02620 2.534987e-34 1.381673e-31 32.26641
PAMR1     83.71323 2.9790698 17.95744 3.456695e-34 1.808681e-31 22.27806
PRDM6     91.47760 1.8387960 17.87196 5.086633e-34 2.559163e-31 17.32527
CEBPD     91.54645 3.4107596 17.77883 7.757076e-34 3.758160e-31 26.00752
DSC3      85.02992 1.9939554 17.58263 1.893786e-33 8.847363e-31 16.57943
NID2      96.15464 3.8234636 17.51582 2.569390e-33 1.158972e-30 28.30090
ATP1B1    47.03459 7.4211313 17.50683 2.677139e-33 1.167322e-30 39.35622
PROM1     72.25689 3.8433103 17.45551 3.385563e-33 1.428598e-30 23.92344
CD248     91.69274 2.2968251 17.43746 3.677205e-33 1.503172e-30 19.37771
MMP1     115.90186 1.3810578 17.38973 4.576444e-33 1.814074e-30 19.03211
CREB3L1   85.06153 3.4812380 17.34846 5.530669e-33 2.127844e-30 24.44471
POSTN    146.69901 3.8513366 17.29813 6.969722e-33 2.604884e-30 33.77001
COL6A3   108.89155 3.4290288 17.18389 1.179448e-32 4.285655e-30 27.68771
BMP4      78.36677 4.6916506 17.09123 1.809374e-32 6.396872e-30 29.29876
DDR2      92.73230 2.8971187 16.82709 6.164394e-32 2.122011e-29 22.27428
SLC40A1   93.69839 3.3828801 16.81543 6.508444e-32 2.182999e-29 25.38491
LRRC32    86.12294 2.2407753 16.73722 9.373010e-32 3.065208e-29 17.33403
AFAP1L2   86.95883 2.6132810 16.51049 2.710205e-31 8.646877e-29 19.15816
KCTD12    87.44824 3.9630040 16.48776 3.015731e-31 9.392566e-29 26.52097
PSD       76.26699 2.9797715 16.37865 5.039793e-31 1.533152e-28 19.04034
COL1A2    91.17029 6.9908439 16.34674 5.858252e-31 1.741632e-28 40.40106
RGS1     102.52738 1.1881097 16.30337 7.189108e-31 2.089794e-28 14.47996
SYT10     95.77620 2.6471171 16.29523 7.470910e-31 2.124499e-28 20.56872
DACT3     65.97882 3.1881491 16.28339 7.900815e-31 2.198948e-28 17.81436
IGFBP3   118.92160 4.8257654 16.19753 1.186010e-30 3.232123e-28 32.89110
HAND1    134.77807 4.6368572 16.13150 1.621890e-30 4.329785e-28 32.94707
SIPA1L2   58.33261 6.1730156 16.11794 1.729646e-30 4.525099e-28 32.74235

$`Stromal cells`
             logFC   AveExpr        t      P.Value    adj.P.Val         B
TNNT2    108.18348 2.9350416 20.58525 3.762754e-39 4.922058e-35 26.142266
COL1A1   117.06049 6.2764999 19.65980 1.908557e-37 1.248292e-33 43.009352
DDR2     107.77230 2.8971187 19.53850 3.218130e-37 1.403212e-33 25.026258
COBLL1    79.47168 3.8078148 19.32050 8.268170e-37 2.703898e-33 24.610660
COL6A3   123.21770 3.4290288 19.09778 2.181581e-36 5.707452e-33 29.484778
CYB5D1    78.79138 3.8300429 18.95405 4.093636e-36 8.924809e-33 23.971441
SLC9A3R1  55.63827 6.6814823 17.53011 2.406958e-33 4.497917e-30 33.306938
DSC3      89.69937 1.9939554 17.25547 8.481054e-33 1.386758e-29 14.313306
PCOLCE    89.36123 4.8474419 17.21487 1.022486e-32 1.486126e-29 28.955816
BMP4      82.04699 4.6916506 16.78545 7.484385e-32 9.790324e-29 26.716740
LUM      139.97848 4.7155844 16.35845 5.543392e-31 6.592101e-28 31.772626
RGS4     116.93518 3.5193512 16.19133 1.221353e-30 1.331377e-27 26.070572
NID2      95.50658 3.8234636 16.03810 2.527523e-30 2.543271e-27 23.599679
COL5A1    85.56052 4.4965267 15.71006 1.210970e-29 1.131479e-26 25.129675
COL3A1   143.18072 5.3883411 15.50759 3.205969e-29 2.795818e-26 32.648309
POSTN    138.85322 3.8513366 14.95951 4.583870e-28 3.747600e-25 26.684269
FGFR2     57.27743 4.9602560 14.78903 1.056183e-27 8.127021e-25 20.827042
COL6A2    78.70748 6.2693029 14.67909 1.812513e-27 1.317194e-24 29.383711
RGS13    136.54020 2.6808708 14.54611 3.489540e-27 2.289248e-24 21.823553
DOK4      58.14475 4.8213956 14.54550 3.500112e-27 2.289248e-24 20.020293
BNC2      80.51735 3.2479340 14.39787 7.260020e-27 4.522301e-24 16.469757
CHN1      60.06911 5.1116585 14.30461 1.152506e-26 6.852694e-24 21.899846
TNNI1    112.23626 3.9575031 13.93017 7.441303e-26 4.232160e-23 22.835920
MFAP4     96.90398 4.0818825 13.87363 9.874933e-26 5.382250e-23 21.712842
TCF21     92.63423 1.8131395 13.82104 1.285212e-25 6.724743e-23 11.169983
ADGRA2    80.55678 2.0801881 13.80508 1.392240e-25 7.004573e-23 10.166371
HAND1    125.69577 4.6368572 13.77658 1.606174e-25 7.781618e-23 25.511846
COL1A2    85.35443 6.9908439 13.75237 1.813669e-25 8.473075e-23 30.829088
DCN      143.40029 3.1437291 13.63822 3.218980e-25 1.451982e-22 22.038099
CYB5A     57.22075 8.2444517 13.61901 3.545817e-25 1.546094e-22 31.435052
CRISPLD2  82.53344 1.9406762 13.57082 4.519746e-25 1.907187e-22  9.667454
CLEC1B   116.42553 0.9545363 13.33793 1.465142e-24 5.989227e-22 10.652023
RPP25     57.71231 4.6152140 13.27267 2.039045e-24 8.082651e-22 17.309567
KCTD12    79.83735 3.9630040 13.20262 2.908709e-24 1.119083e-21 17.672909
CREB3L1   75.63196 3.4812380 13.19183 3.072522e-24 1.148333e-21 14.676387
COL21A1   90.22203 2.4613167 13.16725 3.480838e-24 1.264801e-21 12.524578
PRDM6     79.98501 1.8387960 13.04877 6.357081e-24 2.247486e-21  8.804129
EMILIN1   80.90369 2.8739884 13.04257 6.560920e-24 2.258510e-21 12.459458
HAND2    110.55522 2.7539369 12.98581 8.759329e-24 2.937969e-21 16.871432
AKR1B15   89.95620 1.5067348 12.72707 3.282894e-23 1.073588e-20  7.769805
ATP7B     66.83761 3.0250264 12.68044 4.167975e-23 1.305883e-20 10.326147
PITX1    116.93007 4.7599224 12.67928 4.192883e-23 1.305883e-20 22.903836
AKAP4     88.88907 0.7453011 12.62267 5.603748e-23 1.704712e-20  6.021759
TWIST1    86.62156 3.0945849 12.57185 7.272234e-23 2.162002e-20 14.521911
BAG2      51.54023 4.7561435 12.41755 1.606487e-22 4.669880e-20 15.427152
RGS1      91.25725 1.1881097 12.40382 1.724106e-22 4.902832e-20  7.590996
ACTA2     91.09013 4.4290611 12.22057 4.430902e-22 1.233205e-19 18.733755
GPX8      39.23205 6.1566286 12.14119 6.674252e-22 1.813202e-19 18.927450
COL6A1    56.65777 6.8556861 12.13780 6.792057e-22 1.813202e-19 23.331080
TMEM88    94.80654 6.3716813 12.03416 1.160328e-21 3.035651e-19 24.178627

$`Thymic epithelial cells`
             logFC     AveExpr         t      P.Value    adj.P.Val          B
CER1     193.00176  2.03976580 30.695676 4.059492e-55 5.310221e-51 36.5694701
GYPB     177.99350  0.42110411 25.977722 3.157169e-48 2.064946e-44 23.6216149
APOBEC3G 114.37166  2.09624580 23.010184 2.085013e-43 9.091350e-40 17.9371052
MIXL1    171.00686  2.28064846 22.653002 8.460322e-43 2.766737e-39 29.6043258
PLSCR2   175.71224  1.21188125 22.243069 4.298355e-42 1.124536e-38 25.2961767
SHISAL2B 116.01167  2.60023393 22.043843 9.537185e-42 2.079265e-38 20.6421597
MESP1    145.98008  2.43703522 19.555526 2.990275e-37 5.587969e-34 24.3232941
NTS      147.06861  2.64617511 19.055155 2.628553e-36 4.298012e-33 24.5873159
CYP26A1  147.71944  1.52578314 18.586385 2.072514e-35 3.012285e-32 19.0191666
MESP2    124.06967  1.26059252 17.005968 2.685037e-32 3.512297e-29 12.0882585
GYPE     124.69905  0.55809555 16.261085 8.779308e-31 1.044019e-27  7.9246891
SERPINE2  95.63232  6.36362760 15.135771 1.940941e-28 2.115787e-25 27.8114689
APLNR    133.57700  2.34443547 14.958026 4.617334e-28 4.646104e-25 16.9070604
HS3ST3A1  91.30279  2.11167551 14.884777 6.606422e-28 6.172758e-25  8.6556701
CD48     112.10588  0.33866121 14.663329 1.958592e-27 1.708023e-24  5.3706039
P3H2      77.71862  3.73554197 14.425083 6.345189e-27 5.187588e-24 13.2798296
TRDN     121.88235  2.43023177 14.014042 4.893833e-26 3.765660e-23 14.3395342
SERHL2    96.09632  1.01740361 13.382580 1.168904e-24 8.494684e-22  3.9673889
ARL4D     66.74664  5.51507338 13.226595 2.575631e-24 1.773254e-21 17.9992208
GYPA     107.98440 -0.03156862 12.706006 3.656604e-23 2.391602e-20  2.1105850
EOMES    135.43803  2.44980940 12.472010 1.214226e-22 7.563469e-20 14.3365573
GSC      115.73073  1.21157204 12.360318 2.156584e-22 1.282285e-19  7.0830196
FOXH1    108.41923  3.99993072 12.179629 5.472914e-22 3.112660e-19 15.5705632
CD1D     101.50916  1.51693622 12.139658 6.727143e-22 3.666573e-19  5.1843372
LZTS1     84.78803  2.19411719 12.091050 8.647134e-22 4.524527e-19  5.6812250
GRP      112.31277  0.83584052 11.801895 3.863369e-21 1.943721e-18  4.3560725
FGF17    149.07288  2.12486885 11.692900 6.801665e-21 3.295281e-18 13.7242619
CCDC81    89.03593  2.00758838 11.604642 1.075845e-20 5.026116e-18  5.1481383
FAM24B   114.43025  0.88054893 11.483357 2.021665e-20 9.119105e-18  4.8812022
BMP4      71.13815  4.69165060 11.282778 5.747682e-20 2.506181e-17 11.6999690
TBX6      92.46735  0.91899072 11.273858 6.021319e-20 2.540802e-17  1.6637827
CCKBR     76.72863  2.88643816 11.263807 6.345326e-20 2.593850e-17  6.2252316
ZIC3      75.29811  3.58296979 11.239344 7.208795e-20 2.857523e-17  7.9610729
NR0B1     88.14092  0.75819062 11.207892 8.494137e-20 3.267994e-17  1.5431449
JAKMIP1   88.02260  0.84945015 11.129435 1.279229e-19 4.649940e-17  1.6689264
RFPL2     99.71961  0.13586254 11.129364 1.279702e-19 4.649940e-17  0.9251215
TESC      86.15826  2.45226621 10.872931 4.886840e-19 1.727696e-16  5.2296171
GAL       96.90344  4.49434675 10.750882 9.253526e-19 3.185405e-16 13.6467835
NFKBIA    41.00109  5.55770686 10.562961 2.474797e-18 8.300723e-16  9.7357296
LRRTM1    87.47936  1.16791958 10.486523 3.693181e-18 1.207763e-15  1.7498090
DLL3      59.48401  4.30887700 10.449541 4.482605e-18 1.430170e-15  8.0782715
TMOD1     80.77850  1.92937139 10.239819 1.345007e-17 4.189056e-15  2.8636541
APCDD1L   87.07631  0.73781400 10.013539 4.401784e-17 1.339064e-14  0.4367276
LAPTM4B   33.74561  8.86686851  9.976650 5.340181e-17 1.587611e-14 16.9758623
TUBB2B    37.25719  8.11278211  9.918652 7.235995e-17 2.103423e-14 15.4807605
CKM       87.43050  1.17161988  9.883336 8.706243e-17 2.475791e-14  1.2437795
GATA6     84.79394  4.19882434  9.866547 9.506381e-17 2.645808e-14  9.5972553
HAS2      75.48560  5.59983355  9.795489 1.379148e-16 3.743434e-14 11.9942027
ACSS3     59.09036  3.23960505  9.792316 1.402250e-16 3.743434e-14  3.3384154
VRTN      96.43963  2.17742682  9.734739 1.895526e-16 4.959075e-14  4.7000619

$`Visceral neurons`
             logFC   AveExpr        t      P.Value    adj.P.Val         B
INSM1    143.48626 1.9175950 29.21276 4.796400e-53 6.274171e-49 24.744458
PPP1R17  184.54560 1.8014410 28.93940 1.180041e-52 7.718058e-49 32.844050
GNG3     123.50502 2.6673015 28.45939 5.826723e-52 2.540645e-48 24.352301
ELAVL3   149.72484 2.1343713 27.66509 8.569664e-51 2.802494e-47 26.827052
STMN4    162.39350 1.8398121 27.42875 1.928683e-50 5.045822e-47 28.068321
TLX3     166.65386 0.7263713 26.64117 2.991755e-49 6.522524e-46 22.208885
NHLH1    171.36370 2.4191008 26.08902 2.119770e-48 3.961244e-45 32.121334
SST      213.42537 2.5685871 25.37987 2.740948e-47 4.481793e-44 39.711203
SNCG     169.17925 3.0455669 23.95076 5.584592e-45 8.116895e-42 33.710776
POU4F1   164.98584 1.1963388 23.69237 1.495019e-44 1.955635e-41 22.734270
TLX2     145.10099 0.6052476 23.64412 1.798289e-44 2.138493e-41 14.660848
STMN2    163.01898 4.7054494 23.25301 8.112485e-44 8.843284e-41 42.571324
ELAVL2   130.15549 2.7520644 23.13255 1.294695e-43 1.302762e-40 24.471039
SIX1     167.59031 1.5451431 23.08783 1.540662e-43 1.439528e-40 25.519121
THSD7B   140.24223 0.8857288 22.32679 3.079228e-42 2.685292e-39 14.641737
ADAM11   124.55762 1.3794780 22.23870 4.373923e-42 3.575955e-39 13.827542
DCX      132.88650 2.6276693 22.05566 9.095757e-42 6.998918e-39 23.516234
GAP43    118.28617 4.5145804 21.91289 1.614457e-41 1.173262e-38 31.393742
OLFM1    119.02393 2.7883832 21.67892 4.155562e-41 2.860995e-38 21.073905
NEFL     120.25644 3.6652260 21.59438 5.857186e-41 3.830892e-38 26.908973
RGS10    148.12027 3.1825479 21.53906 7.335332e-41 4.569213e-38 29.335529
CRMP1    109.67937 3.7555245 21.35171 1.576082e-40 9.371237e-38 24.239414
EBF1     144.29651 1.4468041 21.06943 5.029074e-40 2.860231e-37 18.564648
NEUROD1  175.24574 1.6536858 20.74053 1.967234e-39 1.072224e-36 25.563619
TAGLN3   145.55961 3.8492674 20.61828 3.277108e-39 1.714714e-36 31.534294
CCER2    140.68671 0.6853025 20.30846 1.204213e-38 6.058578e-36 12.728506
CACNA1A  101.79501 3.3103615 20.27926 1.362211e-38 6.599661e-36 19.050942
RTN1     129.04158 3.1365014 20.18087 2.065233e-38 9.648325e-36 24.598575
P2RX3    123.10529 0.5999809 20.08437 3.109610e-38 1.402649e-35  9.016660
KLHL35   123.42616 2.1556421 19.95892 5.303060e-38 2.312311e-35 17.729740
RTN4RL2  131.68886 1.3617224 19.89776 6.884279e-38 2.904944e-35 14.281421
INA      107.09496 2.6686304 19.85483 8.270219e-38 3.380710e-35 16.603477
CDKN2D    83.54951 3.4783630 19.30821 8.721599e-37 3.457189e-34 15.527483
TUBB2B    64.95113 8.1127821 19.25257 1.110820e-36 4.273717e-34 38.000339
NEFM     139.27868 3.9768428 19.13767 1.832766e-36 6.849832e-34 29.103516
MAPK8IP1  97.12378 2.9322347 18.58273 2.106376e-35 7.653750e-33 14.703837
NTRK1    133.99739 0.7886271 18.46207 3.600259e-35 1.272838e-32 11.386000
SRRM4    121.29067 1.8829324 18.39436 4.867799e-35 1.675676e-32 14.086560
CD163L1  135.87117 0.3689427 18.11018 1.737174e-34 5.826661e-32  9.110318
EBF3     121.60265 1.2507997 17.88303 4.838159e-34 1.582199e-31  9.823714
SYP      116.31237 1.8687858 17.70193 1.099981e-33 3.509474e-31 12.485281
STMN3    101.55171 3.0624184 17.38022 4.780582e-33 1.488924e-30 15.420668
ISL1     121.27897 3.1288175 17.27599 7.716615e-33 2.347466e-30 20.639316
ONECUT2  123.48408 2.2247446 17.19986 1.095733e-32 3.257564e-30 15.772407
BASP1     66.78895 8.6309172 16.91702 4.056992e-32 1.179323e-29 36.939640
RBFOX3   108.79836 1.6880846 16.69109 1.162742e-31 3.306483e-29  9.291179
PPP1R27  121.14895 0.4451864 16.68133 1.216996e-31 3.387134e-29  5.652912
PRKG1    100.71415 2.9548203 16.59066 1.860503e-31 5.070259e-29 13.676546
TLCD3B   110.89862 1.7731339 16.42595 4.033215e-31 1.076704e-28 10.034900
CELF3    114.68471 1.2546600 16.33571 6.171335e-31 1.614545e-28  8.439524

$scHCL.hESC
              logFC     AveExpr         t      P.Value    adj.P.Val         B
SFRP2      88.47448  4.98786079  29.98283 3.932109e-54 5.143592e-50 69.069262
SOX2       86.08364  4.91896284  27.88873 3.996600e-51 2.613976e-47 66.678658
TUBB2B     39.55603  8.11278211  24.65245 3.994784e-46 1.741859e-42 75.749672
AIF1L      42.65084  4.43344569  22.87440 3.544932e-43 1.159281e-39 55.797943
CENPH      30.15820  5.89862049  22.35249 2.780067e-42 7.273211e-39 63.119952
PSIP1      28.33854  7.78625035  22.21049 4.895163e-42 1.067227e-38 70.201612
MXD4      -33.57232  6.83689314 -21.61983 5.281587e-41 9.869778e-38 63.084482
CDCA7L     39.90071  4.63147355  21.50205 8.528991e-41 1.394597e-37 55.178777
MCM3       28.16851  6.37609094  21.21454 2.766444e-40 4.020872e-37 62.385254
LEPROT    -24.40255  6.67204168 -21.15175 3.581819e-40 4.685378e-37 61.428441
ADD2       57.19132  2.88840658  21.02830 5.959936e-40 7.087447e-37 45.678860
NUDT1      23.40843  6.25338182  20.94338 8.468967e-40 8.745369e-37 61.778780
PDZRN3    -67.72880  3.70102897 -20.93713 8.691216e-40 8.745369e-37 38.221765
GDF3       97.69448  1.59996404  20.81997 1.413393e-39 1.320614e-36 41.223821
MYOF      -65.86157  3.52227670 -20.78941 1.604915e-39 1.321188e-36 35.768940
PARP1      23.27277  8.32541525  20.78776 1.616008e-39 1.321188e-36 67.123967
PAICS      21.93086  7.36177305  20.75609 1.843776e-39 1.418732e-36 65.174341
FOXB1      65.40662  1.17327676  20.38864 8.588984e-39 6.241806e-36 37.571795
SIPA1L2   -51.65337  6.17301564 -20.16709 2.189349e-38 1.484825e-35 52.672560
UNG        30.23598  5.29044745  20.15853 2.270201e-38 1.484825e-35 55.443573
DRAXIN     47.25994  3.38971110  19.86078 8.062656e-38 4.820975e-35 45.823462
DNAJC22   -94.03594  1.55877999 -19.85947 8.108054e-38 4.820975e-35 15.254184
EPSTI1    -73.70485  3.41671521 -19.79922 1.049219e-37 5.967322e-35 32.639722
CLRN3    -154.31051 -0.17763961 -19.67721 1.770897e-37 9.652127e-35  3.213731
EPS8L3   -149.66171  0.08879629 -19.64311 2.050587e-37 1.072949e-34  3.506354
SERPINA4 -162.01529 -0.25042397 -19.60148 2.453034e-37 1.234159e-34  3.027360
OIP5       31.95107  3.84347340  19.56390 2.884195e-37 1.397339e-34 46.674133
AURKB      35.28134  5.17861000  19.39822 5.902328e-37 2.757441e-34 52.676773
PRDM6     -93.68929  1.83879604 -19.22489 1.253043e-36 5.652086e-34 19.881953
SYTL5     -98.93367  2.24499018 -18.96092 3.972123e-36 1.731978e-33 18.278283
WNT11     -86.64629  2.08933026 -18.94104 4.334242e-36 1.828910e-33 21.444003
GLTPD2   -111.87363  0.85038922 -18.84462 6.621945e-36 2.706927e-33  8.194169
HELLS      37.67357  6.54538281  18.80437 7.906349e-36 3.134029e-33 57.218815
ALPL       47.41466  3.83780508  18.79601 8.203432e-36 3.156150e-33 44.644139
ANKS4B   -130.71037  0.24721118 -18.72839 1.105523e-35 4.131812e-33  4.758401
GHR       -80.55263  1.73281284 -18.63844 1.645607e-35 5.979497e-33 20.920098
DEK        21.12288  8.03922184  18.61120 1.856593e-35 6.563810e-33 59.678735
TM4SF5   -156.49140 -0.14786913 -18.57943 2.137395e-35 7.357701e-33  2.998603
F7        -65.00254  1.40758071 -18.51683 2.822126e-35 9.465699e-33 20.417254
SULT2A1  -147.01915  0.03410951 -18.43279 4.101657e-35 1.341344e-32  3.396117
POLR3G     75.99046  3.01002572  18.40034 4.739639e-35 1.512176e-32 42.203558
HP       -134.03382  0.76214284 -18.39385 4.878817e-35 1.519519e-32  5.974937
SMLR1    -109.29633  1.18969314 -18.38294 5.122131e-35 1.558200e-32 10.182044
POU5F1     95.04689  1.07198687  18.36799 5.475388e-35 1.627808e-32 35.375326
HNF4A    -113.17626  1.21622595 -18.35007 5.931185e-35 1.724129e-32 11.934774
CHAF1A     29.48863  5.39328572  18.33970 6.212265e-35 1.766579e-32 50.978346
MYLK3     -79.76192  1.47854340 -18.32711 6.571658e-35 1.829018e-32 18.850828
LHX1     -132.32825  0.18853835 -18.31336 6.988050e-35 1.904389e-32  4.296949
MYRF      -63.06571  3.18296951 -18.29571 7.561781e-35 1.978685e-32 31.527621
CDCA5      33.53810  4.23890971  18.29567 7.563202e-35 1.978685e-32 45.848079

checking for top DE markers from Cao and descartes browser

#metanephric: EYA1, UNCX, LRP2, NKAIN3, TMEM132D
 tab<- topTable(efit, coef=14, sort.by="P", n=2000)
tab[rownames(tab) %in% c("EYA1", "UNCX", "LRP2", "NKAIN3", "TMEM132D", "IGF2", "AUTS2", "DACH1", "ROBO2", "H19", "PTPRG", "ERBB4", "NCAM", "FZD7", "SIX2", "OSR1", "WT1", "PAX2", "MEOX1", "MEIS1", "MEIS2"),]

          logFC  AveExpr         t      P.Value    adj.P.Val          B
IGF2  132.18863 3.400974 17.139198 1.449645e-32 3.577889e-30 30.2514297
AUTS2 -37.07923 4.939878 -5.843750 5.496029e-08 1.018322e-06 -1.7166855
ERBB4  54.65935 3.671931  5.325014 5.555282e-07 8.808320e-06  0.6774518
ROBO2 -40.11892 4.068405 -3.298405 1.317749e-03 8.683867e-03 -3.8271393

FeaturePlot(merged, features=c("EYA1", "UNCX", "LRP2", "NKAIN3", "TMEM132D"))

#hepatoblasts: SLC2A25, ACSS2, ASSI. SLC2A25 and ASS1 are not in our data set
 tab<- topTable(efit, coef=8, sort.by="P", n=2000)
tab[rownames(tab) %in% c("SLC2A25", "ACSS2", "ASSI", "DLK1", "KRT18", "KRT8"),]

         logFC  AveExpr        t      P.Value    adj.P.Val        B
ACSS2 62.36734 3.254362 16.01529 2.817248e-30 1.349905e-28 19.19883

vol<- topTable(efit, coef=8, n=nrow(fit))
labsig<- vol[rownames(vol) %in% c("AFP", "FGB", "ACSS2"),]
labsiggenes<- rownames(labsig)
thresh<- vol$adj.P.Val < 0.05
vol<-cbind(vol, thresh)
b<- ggplot(vol, aes(x=logFC, y= -log10(adj.P.Val))) +
  geom_point(aes(colour=thresh), show.legend = FALSE) +
  scale_colour_manual(values = c("TRUE" = "red", "FALSE" = "black")) +
  geom_text(data=labsig, aes(label=labsiggenes))

b

png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Supp_RefAnnDE_hepatoblast.png", width= 6, height=6, units= "in", res= 1080)

b

dev.off()

#amacrine: MEIS2
 tab<- topTable(efit, coef=1, sort.by="P", n=2000)
tab[rownames(tab) %in% c("MEIS2"),]

[1] logFC     AveExpr   t         P.Value   adj.P.Val B        
<0 rows> (or 0-length row.names)

mesothelial

vol<- topTable(efit, coef=13, n=nrow(fit))
labsig<- vol[rownames(vol) %in% c("NID2", "COL6A3", "COL1A1", "COL3A1", "COL6A1"),]
labsiggenes<- rownames(labsig)
thresh<- vol$adj.P.Val < 0.05
vol<-cbind(vol, thresh)
p<- ggplot(vol, aes(x=logFC, y= -log10(adj.P.Val))) +
  geom_point(aes(colour=thresh), show.legend = FALSE) +
  scale_colour_manual(values = c("TRUE" = "red", "FALSE" = "black")) +
  geom_text(data=labsig, aes(label=labsiggenes))

p

png(file= "/project2/gilad/katie/Pilot_HumanEBs/Embryoid_Body_Pilot_Workflowr/output/figs/Supp_RefAnnDE_mesothelial.png", width= 6, height=6, units= "in", res= 1080)

p

dev.off()

sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
[1] C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] scater_1.14.6               ggplot2_3.3.3              
 [3] SingleCellExperiment_1.8.0  SummarizedExperiment_1.16.1
 [5] DelayedArray_0.12.3         BiocParallel_1.20.1        
 [7] matrixStats_0.57.0          Biobase_2.46.0             
 [9] GenomicRanges_1.38.0        GenomeInfoDb_1.22.1        
[11] IRanges_2.20.2              S4Vectors_0.24.4           
[13] BiocGenerics_0.32.0         dplyr_1.0.2                
[15] Matrix_1.2-18               edgeR_3.28.1               
[17] limma_3.42.2                Seurat_3.2.0               
[19] workflowr_1.6.2            

loaded via a namespace (and not attached):
  [1] plyr_1.8.6               igraph_1.2.6             lazyeval_0.2.2          
  [4] splines_3.6.1            listenv_0.8.0            digest_0.6.27           
  [7] htmltools_0.5.0          viridis_0.5.1            gdata_2.18.0            
 [10] magrittr_2.0.1           tensor_1.5               cluster_2.1.0           
 [13] ROCR_1.0-7               globals_0.12.5           colorspace_2.0-0        
 [16] rappdirs_0.3.3           ggrepel_0.9.0            xfun_0.16               
 [19] crayon_1.3.4             RCurl_1.98-1.2           jsonlite_1.7.2          
 [22] spatstat_1.64-1          spatstat.data_1.4-3      survival_3.2-3          
 [25] zoo_1.8-8                ape_5.4-1                glue_1.4.2              
 [28] polyclip_1.10-0          gtable_0.3.0             zlibbioc_1.32.0         
 [31] XVector_0.26.0           leiden_0.3.3             BiocSingular_1.2.2      
 [34] future.apply_1.6.0       abind_1.4-5              scales_1.1.1            
 [37] miniUI_0.1.1.1           Rcpp_1.0.6               viridisLite_0.3.0       
 [40] xtable_1.8-4             reticulate_1.20          rsvd_1.0.3              
 [43] htmlwidgets_1.5.1        httr_1.4.2               gplots_3.0.4            
 [46] RColorBrewer_1.1-2       ellipsis_0.3.1           ica_1.0-2               
 [49] farver_2.0.3             pkgconfig_2.0.3          uwot_0.1.10             
 [52] deldir_0.1-28            locfit_1.5-9.4           labeling_0.4.2          
 [55] tidyselect_1.1.0         rlang_0.4.10             reshape2_1.4.4          
 [58] later_1.1.0.1            munsell_0.5.0            tools_3.6.1             
 [61] generics_0.1.0           ggridges_0.5.2           evaluate_0.14           
 [64] stringr_1.4.0            fastmap_1.0.1            yaml_2.2.1              
 [67] goftest_1.2-2            npsurv_0.4-0             knitr_1.29              
 [70] fs_1.4.2                 fitdistrplus_1.0-14      caTools_1.18.0          
 [73] purrr_0.3.4              RANN_2.6.1               pbapply_1.4-2           
 [76] future_1.18.0            nlme_3.1-140             mime_0.9                
 [79] compiler_3.6.1           beeswarm_0.2.3           plotly_4.9.2.1          
 [82] png_0.1-7                lsei_1.2-0               spatstat.utils_1.17-0   
 [85] tibble_3.0.4             stringi_1.5.3            highr_0.8               
 [88] lattice_0.20-38          vctrs_0.3.6              pillar_1.4.7            
 [91] lifecycle_0.2.0          lmtest_0.9-37            RcppAnnoy_0.0.18        
 [94] BiocNeighbors_1.4.2      data.table_1.13.4        cowplot_1.1.1           
 [97] bitops_1.0-6             irlba_2.3.3              httpuv_1.5.4            
[100] patchwork_1.1.1          R6_2.5.0                 promises_1.1.1          
[103] KernSmooth_2.23-15       gridExtra_2.3            vipor_0.4.5             
[106] codetools_0.2-16         MASS_7.3-51.4            gtools_3.8.2            
[109] rprojroot_2.0.2          withr_2.4.2              sctransform_0.2.1       
[112] GenomeInfoDbData_1.2.2   mgcv_1.8-28              grid_3.6.1              
[115] rpart_4.1-15             tidyr_1.1.0              DelayedMatrixStats_1.8.0
[118] rmarkdown_2.3            Rtsne_0.15               git2r_0.26.1            
[121] shiny_1.5.0              ggbeeswarm_0.6.0        

Session information

sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
[1] C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] scater_1.14.6               ggplot2_3.3.3              
 [3] SingleCellExperiment_1.8.0  SummarizedExperiment_1.16.1
 [5] DelayedArray_0.12.3         BiocParallel_1.20.1        
 [7] matrixStats_0.57.0          Biobase_2.46.0             
 [9] GenomicRanges_1.38.0        GenomeInfoDb_1.22.1        
[11] IRanges_2.20.2              S4Vectors_0.24.4           
[13] BiocGenerics_0.32.0         dplyr_1.0.2                
[15] Matrix_1.2-18               edgeR_3.28.1               
[17] limma_3.42.2                Seurat_3.2.0               
[19] workflowr_1.6.2            

loaded via a namespace (and not attached):
  [1] plyr_1.8.6               igraph_1.2.6             lazyeval_0.2.2          
  [4] splines_3.6.1            listenv_0.8.0            digest_0.6.27           
  [7] htmltools_0.5.0          viridis_0.5.1            gdata_2.18.0            
 [10] magrittr_2.0.1           tensor_1.5               cluster_2.1.0           
 [13] ROCR_1.0-7               globals_0.12.5           colorspace_2.0-0        
 [16] rappdirs_0.3.3           ggrepel_0.9.0            xfun_0.16               
 [19] crayon_1.3.4             RCurl_1.98-1.2           jsonlite_1.7.2          
 [22] spatstat_1.64-1          spatstat.data_1.4-3      survival_3.2-3          
 [25] zoo_1.8-8                ape_5.4-1                glue_1.4.2              
 [28] polyclip_1.10-0          gtable_0.3.0             zlibbioc_1.32.0         
 [31] XVector_0.26.0           leiden_0.3.3             BiocSingular_1.2.2      
 [34] future.apply_1.6.0       abind_1.4-5              scales_1.1.1            
 [37] miniUI_0.1.1.1           Rcpp_1.0.6               viridisLite_0.3.0       
 [40] xtable_1.8-4             reticulate_1.20          rsvd_1.0.3              
 [43] htmlwidgets_1.5.1        httr_1.4.2               gplots_3.0.4            
 [46] RColorBrewer_1.1-2       ellipsis_0.3.1           ica_1.0-2               
 [49] farver_2.0.3             pkgconfig_2.0.3          uwot_0.1.10             
 [52] deldir_0.1-28            locfit_1.5-9.4           labeling_0.4.2          
 [55] tidyselect_1.1.0         rlang_0.4.10             reshape2_1.4.4          
 [58] later_1.1.0.1            munsell_0.5.0            tools_3.6.1             
 [61] generics_0.1.0           ggridges_0.5.2           evaluate_0.14           
 [64] stringr_1.4.0            fastmap_1.0.1            yaml_2.2.1              
 [67] goftest_1.2-2            npsurv_0.4-0             knitr_1.29              
 [70] fs_1.4.2                 fitdistrplus_1.0-14      caTools_1.18.0          
 [73] purrr_0.3.4              RANN_2.6.1               pbapply_1.4-2           
 [76] future_1.18.0            nlme_3.1-140             mime_0.9                
 [79] compiler_3.6.1           beeswarm_0.2.3           plotly_4.9.2.1          
 [82] png_0.1-7                lsei_1.2-0               spatstat.utils_1.17-0   
 [85] tibble_3.0.4             stringi_1.5.3            highr_0.8               
 [88] lattice_0.20-38          vctrs_0.3.6              pillar_1.4.7            
 [91] lifecycle_0.2.0          lmtest_0.9-37            RcppAnnoy_0.0.18        
 [94] BiocNeighbors_1.4.2      data.table_1.13.4        cowplot_1.1.1           
 [97] bitops_1.0-6             irlba_2.3.3              httpuv_1.5.4            
[100] patchwork_1.1.1          R6_2.5.0                 promises_1.1.1          
[103] KernSmooth_2.23-15       gridExtra_2.3            vipor_0.4.5             
[106] codetools_0.2-16         MASS_7.3-51.4            gtools_3.8.2            
[109] rprojroot_2.0.2          withr_2.4.2              sctransform_0.2.1       
[112] GenomeInfoDbData_1.2.2   mgcv_1.8-28              grid_3.6.1              
[115] rpart_4.1-15             tidyr_1.1.0              DelayedMatrixStats_1.8.0
[118] rmarkdown_2.3            Rtsne_0.15               git2r_0.26.1            
[121] shiny_1.5.0              ggbeeswarm_0.6.0