---
title: "PADDI RNA expression downstream analysis"
author: "Mark Ziemann"
date: "2026-06-01"
output:
html_document:
toc: true
toc_float: true
fig_width: 7
fig_height: 7
theme: cosmo
---
## Introduction
The differential analysis was already conducted using the qc.Rmd script.
Here we are doing downstream analysis including pathway analysis and charts.
``` r
suppressPackageStartupMessages({
library("gplots")
library("reshape2")
library("WGCNA")
library("dplyr")
library("DESeq2")
library("mitch")
library("MASS")
library("kableExtra")
library("ggplot2")
library("eulerr")
library("DT")
library("xlsx")
library("RhpcBLASctl")
})
load("qc.Rds")
RhpcBLASctl::blas_set_num_threads(1)
knitr::opts_chunk$set(dev = 'svg') # set output device to svg
```
## Functions
``` r
volcanoplot <- function(x,title) {
tot <- nrow(x)
sig <- subset(x,padj<0.05)
nsig <- nrow(subset(x,padj<0.05))
dn <- nrow(subset(x,padj<0.05 & log2FoldChange<0))
up <- nrow(subset(x,padj<0.05 & log2FoldChange>0))
header <- paste(title,":", tot, "genes,", nsig ,"@5% FDR,", up, "up,", dn, "dn")
plot(x$log2FoldChange,-log10(x$pvalue),bty="n",
cex=0.5, pch=19, xlab="log2 fold change",
ylab="-log10 p-value", main=header)
points(sig$log2FoldChange,-log10(sig$pvalue),
cex=0.5, pch=19, col="red")
}
smearplot <- function(x,title) {
tot <- nrow(x)
sig <- subset(x,padj<0.05)
nsig <- nrow(subset(x,padj<0.05))
dn <- nrow(subset(x,padj<0.05 & log2FoldChange<0))
up <- nrow(subset(x,padj<0.05 & log2FoldChange>0))
header <- paste(title,":", tot, "genes,", nsig ,"@5% FDR,", up, "up,", dn, "dn")
plot(log10(x$baseMean),x$log2FoldChange,bty="n",
cex=0.5, pch=19, xlab="log10 base mean",
ylab="log2 fold change", main=header)
points(log10(sig$baseMean),sig$log2FoldChange,
cex=0.5, pch=19, col="red")
}
debar <- function(l) {
nn <- sapply(l,function(x) {
nup <- nrow(subset(x,padj<0.05 & log2FoldChange>0 ))
ndn <- nrow(subset(x,padj<0.05 & log2FoldChange<0 )) *-1
return(c(nup,ndn))
})
rownames(nn) <- c("up","dn")
par(mar = c(8.1, 4.1, 4.1, 2.1))
barplot(nn[1,],col="blue",beside = TRUE, border=TRUE,ylim=c(min(nn),max(nn)) , las=2)
barplot(nn[2,],add=TRUE,col="red",names.arg = "", ylab="", yaxt="n")
mtext("blue=up,red=down")
par(mar = c(5.1, 4.1, 4.1, 2.1))
}
myeuler <- function(l) {
ups <- lapply(l,function(x) { rownames(subset(x,padj<0.05 & log2FoldChange>0) )})
dns <- lapply(l,function(x) { rownames(subset(x,padj<0.05 & log2FoldChange<0) )})
names(ups) <- paste(names(ups),"up")
names(dns) <- paste(names(dns),"dn")
ll <- c(ups,dns)
plot(euler(ll),quantities = TRUE)
}
writeTSV <- function(l) {
lapply(1:length(l), function(i) {
filename <- paste(names(l)[i],".tsv",sep="")
write.table(x=l[[i]],file=filename,sep="\t",quote=FALSE)
})
}
```
## DE results
### Unadjusted for clinical covariates
#### Unstratified, unadjusted
* crp_t0
* crp_eos
* crp_pod1
* dex_t0
* dex_eos
* dex_pod1
``` r
l1 <- list("crp_t0"=crp_t0, "crp_eos"=crp_eos, "crp_pod1"=crp_pod1,
"dex_t0"=dex_t0,"dex_eos"=dex_eos,"dex_pod1"=dex_pod1 )
lapply(1:length(l1),function(i) {
volcanoplot(x=l1[[i]], title=names(l1)[[i]])
smearplot(x=l1[[i]], title=names(l1)[[i]])
print( head(l1[[i]],50) |>
kbl(caption = paste(names(l1)[[i]],"top 50 genes")) |>
kable_paper("hover", full_width = F))
} )
```
```
## [[1]]
##
## [[2]]
##
## [[3]]
##
## [[4]]
##
## [[5]]
##
## [[6]]
```
``` r
debar(l1) ; par(mar = c(5.1, 4.1, 4.1, 2.1))
```
``` r
myeuler(list("crp_t0"=crp_t0,"crp_eos"=crp_eos))
```
``` r
myeuler(list("crp_eos"=crp_eos,"crp_pod1"=crp_pod1))
```
``` r
myeuler(list("dex_t0"=dex_t0,"dex_eos"=dex_eos))
```
``` r
myeuler(list("dex_eos"=dex_eos,"dex_pod1"=dex_pod1))
```
``` r
myeuler(list("crp_t0"=crp_t0,"dex_t0"=dex_t0))
```
``` r
myeuler(list("crp_eos"=crp_eos,"dex_eos"=dex_eos))
```
``` r
myeuler(list("crp_pod1"=crp_pod1,"dex_pod1"=dex_pod1))
```
``` r
myeuler(list("crp_pod1"=crp_pod1,"dex_eos"=dex_eos))
```
``` r
message("crp_t0")
```
```
## crp_t0
```
``` r
datatable(crp_t0[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_eos")
```
```
## crp_eos
```
``` r
datatable(crp_eos[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_pod1")
```
```
## crp_pod1
```
``` r
datatable(crp_pod1[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_t0")
```
```
## dex_t0
```
``` r
datatable(dex_t0[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_eos")
```
```
## dex_eos
```
``` r
datatable(dex_eos[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_pod1")
```
```
## dex_pod1
```
``` r
datatable(dex_pod1[1:1000,1:6])
```
```{=html}
```
``` r
intersect( rownames(subset(dex_eos,padj<0.05 & log2FoldChange>0)) , rownames(subset(crp_eos,padj<0.05 & log2FoldChange>0)) )
```
```
## [1] "ENSG00000183873.18 SCN5A" "ENSG00000123836.15 PFKFB2"
## [3] "ENSG00000122642.11 FKBP9" "ENSG00000198929.13 NOS1AP"
## [5] "ENSG00000273812.3 WI2-87327B8.2" "ENSG00000079156.17 OSBPL6"
## [7] "ENSG00000064270.13 ATP2C2" "ENSG00000251139.2 RP11-701P16.2"
```
``` r
intersect( rownames(subset(dex_eos,padj<0.05 & log2FoldChange<0)) , rownames(subset(crp_eos,padj<0.05 & log2FoldChange<0)) )
```
```
## character(0)
```
``` r
intersect( rownames(subset(dex_eos,padj<0.05 & log2FoldChange>0)) , rownames(subset(crp_eos,padj<0.05 & log2FoldChange<0)) )
```
```
## [1] "ENSG00000141744.4 PNMT" "ENSG00000135678.12 CPM"
## [3] "ENSG00000155659.15 VSIG4" "ENSG00000166979.13 EVA1C"
## [5] "ENSG00000197892.13 KIF13B" "ENSG00000105255.11 FSD1"
## [7] "ENSG00000158485.11 CD1B" "ENSG00000129596.5 CDO1"
## [9] "ENSG00000238121.6 LINC00426" "ENSG00000196542.8 SPTSSB"
## [11] "ENSG00000137831.15 UACA" "ENSG00000156804.7 FBXO32"
## [13] "ENSG00000185418.16 TARS3" "ENSG00000179859.10 RNF227"
## [15] "ENSG00000170873.19 MTSS1" "ENSG00000185432.12 METTL7A"
## [17] "ENSG00000171657.6 GPR82" "ENSG00000279841.1 RP11-274A11.4"
## [19] "ENSG00000105246.6 EBI3" "ENSG00000088726.16 TMEM40"
## [21] "ENSG00000286633.1 RP11-367G6.4" "ENSG00000211946.3 IGHV3-20"
## [23] "ENSG00000108091.11 CCDC6" "ENSG00000111186.13 WNT5B"
## [25] "ENSG00000238062.6 SPATA3-AS1" "ENSG00000105717.14 PBX4"
## [27] "ENSG00000134853.12 PDGFRA" "ENSG00000214922.9 HLA-F-AS1"
## [29] "ENSG00000240497.3 RP11-185E8.1" "ENSG00000136944.19 LMX1B"
## [31] "ENSG00000169313.10 P2RY12" "ENSG00000253305.2 PCDHGB6"
## [33] "ENSG00000225936.1 RP11-501J20.5" "ENSG00000151789.12 ZNF385D"
## [35] "ENSG00000278828.1 H3C10" "ENSG00000232125.5 DYTN"
## [37] "ENSG00000204624.8 DISP3" "ENSG00000101856.10 PGRMC1"
## [39] "ENSG00000123739.11 PLA2G12A" "ENSG00000130340.17 SNX9"
## [41] "ENSG00000277435.1 RP11-1180F24.1" "ENSG00000205531.13 NAP1L4"
## [43] "ENSG00000158488.16 CD1E" "ENSG00000119684.16 MLH3"
## [45] "ENSG00000211459.2 MT-RNR1" "ENSG00000266401.2 RP11-874J12.4"
## [47] "ENSG00000153347.10 FAM81B" "ENSG00000143595.13 AQP10"
## [49] "ENSG00000267279.2 RP11-879F14.2" "ENSG00000204323.5 SMIM5"
## [51] "ENSG00000210082.2 MT-RNR2" "ENSG00000050393.11 MCUR1"
## [53] "ENSG00000237973.1 MTCO1P12" "ENSG00000211933.2 IGHV6-1"
## [55] "ENSG00000243290.3 IGKV1-12" "ENSG00000277075.2 H2AC8"
## [57] "ENSG00000211675.2 IGLC1" "ENSG00000267364.2 RP11-47L3.1"
## [59] "ENSG00000283907.1 LLNLF-96A1.1" "ENSG00000272979.1 RP11-647K16.1"
## [61] "ENSG00000228474.6 OST4" "ENSG00000166681.14 BEX3"
## [63] "ENSG00000171793.16 CTPS1" "ENSG00000279970.1 RP11-299G20.5"
## [65] "ENSG00000211651.3 IGLV1-44" "ENSG00000211890.4 IGHA2"
## [67] "ENSG00000148908.15 RGS10" "ENSG00000176903.5 PNMA1"
## [69] "ENSG00000280614.1 CH507-513H4.4" "ENSG00000280800.1 CH507-513H4.6"
## [71] "ENSG00000281181.1 CH507-513H4.3" "ENSG00000211644.3 IGLV1-51"
```
``` r
intersect( rownames(subset(dex_eos,padj<0.05 & log2FoldChange<0)) , rownames(subset(crp_eos,padj<0.05 & log2FoldChange>0)) )
```
```
## [1] "ENSG00000054965.11 FAM168A" "ENSG00000133805.15 AMPD3"
## [3] "ENSG00000089057.15 SLC23A2" "ENSG00000111642.16 CHD4"
## [5] "ENSG00000159110.21 IFNAR2" "ENSG00000285103.2 RP11-27J8.3"
## [7] "ENSG00000095951.17 HIVEP1" "ENSG00000272839.1 RP11-452C13.1"
## [9] "ENSG00000135407.10 AVIL" "ENSG00000136960.13 ENPP2"
## [11] "ENSG00000119408.17 NEK6" "ENSG00000167604.15 NFKBID"
## [13] "ENSG00000277443.3 MARCKS" "ENSG00000143318.13 CASQ1"
## [15] "ENSG00000143067.5 ZNF697" "ENSG00000185650.10 ZFP36L1"
## [17] "ENSG00000283155.1 AC011380.9" "ENSG00000171608.16 PIK3CD"
## [19] "ENSG00000120889.13 TNFRSF10B" "ENSG00000143437.21 ARNT"
## [21] "ENSG00000186350.12 RXRA" "ENSG00000166401.15 SERPINB8"
## [23] "ENSG00000122547.11 EEPD1" "ENSG00000033627.17 ATP6V0A1"
## [25] "ENSG00000160712.13 IL6R" "ENSG00000109320.13 NFKB1"
## [27] "ENSG00000178996.14 SNX18" "ENSG00000167208.15 SNX20"
## [29] "ENSG00000163823.4 CCR1" "ENSG00000132681.17 ATP1A4"
## [31] "ENSG00000058866.15 DGKG" "ENSG00000160584.17 SIK3"
## [33] "ENSG00000136689.19 IL1RN" "ENSG00000249835.2 VCAN-AS1"
## [35] "ENSG00000197632.9 SERPINB2" "ENSG00000140749.9 IGSF6"
## [37] "ENSG00000116711.10 PLA2G4A" "ENSG00000204131.9 NHSL2"
## [39] "ENSG00000165458.14 INPPL1" "ENSG00000223177.1 RNA5SP39"
## [41] "ENSG00000127954.13 STEAP4" "ENSG00000173530.6 TNFRSF10D"
## [43] "ENSG00000139083.11 ETV6"
```
``` r
intersect( rownames(subset(dex_pod1,padj<0.05 & log2FoldChange>0)) , rownames(subset(crp_pod1,padj<0.05 & log2FoldChange>0)) )
```
```
## character(0)
```
``` r
intersect( rownames(subset(dex_pod1,padj<0.05 & log2FoldChange<0)) , rownames(subset(crp_pod1,padj<0.05 & log2FoldChange<0)) )
```
```
## character(0)
```
``` r
intersect( rownames(subset(dex_pod1,padj<0.05 & log2FoldChange>0)) , rownames(subset(crp_pod1,padj<0.05 & log2FoldChange<0)) )
```
```
## [1] "ENSG00000115414.21 FN1" "ENSG00000163050.18 COQ8A"
## [3] "ENSG00000049089.15 COL9A2" "ENSG00000165457.14 FOLR2"
## [5] "ENSG00000158485.11 CD1B" "ENSG00000214063.11 TSPAN4"
## [7] "ENSG00000165092.13 ALDH1A1" "ENSG00000091592.16 NLRP1"
## [9] "ENSG00000181885.18 CLDN7" "ENSG00000158488.16 CD1E"
## [11] "ENSG00000055957.11 ITIH1" "ENSG00000187166.1 H1-7"
## [13] "ENSG00000175262.14 C1orf127" "ENSG00000074660.16 SCARF1"
## [15] "ENSG00000170275.15 CRTAP" "ENSG00000237225.2 OR13K1P"
## [17] "ENSG00000215067.10 ALOX12-AS1" "ENSG00000259431.6 THTPA"
## [19] "ENSG00000168906.13 MAT2A" "ENSG00000237973.1 MTCO1P12"
## [21] "ENSG00000055955.17 ITIH4" "ENSG00000010318.21 PHF7"
```
``` r
intersect( rownames(subset(dex_pod1,padj<0.05 & log2FoldChange<0)) , rownames(subset(crp_pod1,padj<0.05 & log2FoldChange>0)) )
```
```
## [1] "ENSG00000179348.12 GATA2" "ENSG00000105855.10 ITGB8"
## [3] "ENSG00000136960.13 ENPP2" "ENSG00000244300.3 GATA2-AS1"
## [5] "ENSG00000211891.6 IGHE" "ENSG00000263006.6 ROCK1P1"
## [7] "ENSG00000258227.7 CLEC5A" "ENSG00000089685.15 BIRC5"
## [9] "ENSG00000135218.19 CD36" "ENSG00000099139.14 PCSK5"
## [11] "ENSG00000169994.19 MYO7B" "ENSG00000145287.11 PLAC8"
## [13] "ENSG00000050628.20 PTGER3" "ENSG00000117724.13 CENPF"
## [15] "ENSG00000257017.9 HP" "ENSG00000152766.6 ANKRD22"
## [17] "ENSG00000172594.13 SMPDL3A" "ENSG00000164741.15 DLC1"
## [19] "ENSG00000198018.7 ENTPD7" "ENSG00000138180.16 CEP55"
## [21] "ENSG00000287367.1 CTD-2591A1.2" "ENSG00000148773.14 MKI67"
## [23] "ENSG00000007968.7 E2F2" "ENSG00000168306.13 ACOX2"
## [25] "ENSG00000196878.15 LAMB3" "ENSG00000111880.16 RNGTT"
## [27] "ENSG00000147570.10 DNAJC5B" "ENSG00000242550.6 SERPINB10"
## [29] "ENSG00000133101.10 CCNA1" "ENSG00000074181.9 NOTCH3"
## [31] "ENSG00000136231.14 IGF2BP3" "ENSG00000101425.14 BPI"
```
``` r
intersect( rownames(subset(dex_eos,padj<0.05 & log2FoldChange>0)) , rownames(subset(crp_pod1,padj<0.05 & log2FoldChange>0)) )
```
```
## [1] "ENSG00000079215.15 SLC1A3" "ENSG00000101187.16 SLCO4A1"
## [3] "ENSG00000174705.13 SH3PXD2B" "ENSG00000185338.7 SOCS1"
## [5] "ENSG00000169860.7 P2RY1" "ENSG00000096060.15 FKBP5"
## [7] "ENSG00000198363.18 ASPH" "ENSG00000106070.20 GRB10"
## [9] "ENSG00000179241.13 LDLRAD3" "ENSG00000164120.14 HPGD"
## [11] "ENSG00000170776.22 AKAP13" "ENSG00000064393.16 HIPK2"
## [13] "ENSG00000103257.9 SLC7A5" "ENSG00000134198.10 TSPAN2"
## [15] "ENSG00000169826.8 CSGALNACT2" "ENSG00000258867.6 LINC01146"
## [17] "ENSG00000108219.15 TSPAN14" "ENSG00000105352.10 CEACAM4"
## [19] "ENSG00000115590.14 IL1R2" "ENSG00000287458.1 RP3-340B19.7"
## [21] "ENSG00000183696.14 UPP1" "ENSG00000129673.10 AANAT"
## [23] "ENSG00000143119.14 CD53" "ENSG00000224721.1 AC007182.6"
## [25] "ENSG00000133101.10 CCNA1" "ENSG00000107968.10 MAP3K8"
## [27] "ENSG00000233608.4 TWIST2" "ENSG00000042062.13 RIPOR3"
## [29] "ENSG00000141298.19 SSH2" "ENSG00000062598.18 ELMO2"
## [31] "ENSG00000102755.12 FLT1" "ENSG00000227268.5 KLLN"
## [33] "ENSG00000196396.10 PTPN1" "ENSG00000134668.12 SPOCD1"
## [35] "ENSG00000155926.14 SLA" "ENSG00000229647.2 MYOSLID"
## [37] "ENSG00000287736.1 PTCSC1" "ENSG00000115604.12 IL18R1"
## [39] "ENSG00000108582.12 CPD" "ENSG00000101447.15 FAM83D"
## [41] "ENSG00000107566.14 ERLIN1" "ENSG00000163734.4 CXCL3"
## [43] "ENSG00000196083.10 IL1RAP" "ENSG00000253214.2 RP11-1149M10.2"
## [45] "ENSG00000275302.2 CCL4" "ENSG00000064999.15 ANKS1A"
## [47] "ENSG00000085741.13 WNT11" "ENSG00000132170.24 PPARG"
## [49] "ENSG00000067900.8 ROCK1" "ENSG00000148175.13 STOM"
## [51] "ENSG00000155307.19 SAMSN1" "ENSG00000135048.14 CEMIP2"
## [53] "ENSG00000140859.16 KIFC3" "ENSG00000145703.16 IQGAP2"
## [55] "ENSG00000277632.2 CCL3" "ENSG00000121964.15 GTDC1"
## [57] "ENSG00000236525.1 AC007278.2" "ENSG00000118263.15 KLF7"
## [59] "ENSG00000123983.15 ACSL3" "ENSG00000120885.22 CLU"
## [61] "ENSG00000158352.17 SHROOM4" "ENSG00000184005.11 ST6GALNAC3"
## [63] "ENSG00000067064.12 IDI1" "ENSG00000283036.3 LINC01988"
## [65] "ENSG00000116991.11 SIPA1L2" "ENSG00000112576.13 CCND3"
## [67] "ENSG00000153071.15 DAB2" "ENSG00000123836.15 PFKFB2"
## [69] "ENSG00000154359.13 LONRF1" "ENSG00000249867.6 LINC02742"
## [71] "ENSG00000263370.1 RP11-68I3.5" "ENSG00000120899.18 PTK2B"
## [73] "ENSG00000111885.7 MAN1A1" "ENSG00000232043.1 RP4-530I15.9"
## [75] "ENSG00000170017.12 ALCAM" "ENSG00000076641.4 PAG1"
## [77] "ENSG00000100906.11 NFKBIA" "ENSG00000186591.13 UBE2H"
## [79] "ENSG00000111913.20 RIPOR2" "ENSG00000146376.11 ARHGAP18"
## [81] "ENSG00000136158.12 SPRY2" "ENSG00000107338.10 SHB"
## [83] "ENSG00000138316.11 ADAMTS14" "ENSG00000157064.11 NMNAT2"
## [85] "ENSG00000163659.13 TIPARP" "ENSG00000167634.12 NLRP7"
## [87] "ENSG00000003402.20 CFLAR" "ENSG00000118503.15 TNFAIP3"
## [89] "ENSG00000162407.9 PLPP3" "ENSG00000166265.13 CYYR1"
## [91] "ENSG00000164104.12 HMGB2" "ENSG00000185022.12 MAFF"
## [93] "ENSG00000233559.2 LINC00513" "ENSG00000116016.14 EPAS1"
## [95] "ENSG00000100731.16 PCNX1" "ENSG00000198929.13 NOS1AP"
## [97] "ENSG00000248975.2 CTD-2251F13.1" "ENSG00000235192.1 AC009495.2"
## [99] "ENSG00000118520.15 ARG1" "ENSG00000068024.17 HDAC4"
## [101] "ENSG00000224177.8 LINC00570" "ENSG00000188305.6 PEAK3"
## [103] "ENSG00000067066.17 SP100" "ENSG00000152766.6 ANKRD22"
## [105] "ENSG00000286236.1 LLNLR-470E3.2" "ENSG00000157557.13 ETS2"
## [107] "ENSG00000151014.6 NOCT" "ENSG00000163602.11 RYBP"
## [109] "ENSG00000137393.10 RNF144B" "ENSG00000126803.10 HSPA2"
## [111] "ENSG00000140563.15 MCTP2" "ENSG00000273812.3 WI2-87327B8.2"
## [113] "ENSG00000287134.1 RP11-183J19.1" "ENSG00000173744.18 AGFG1"
## [115] "ENSG00000164741.15 DLC1" "ENSG00000064270.13 ATP2C2"
## [117] "ENSG00000164796.18 CSMD3" "ENSG00000182118.8 FAM89A"
## [119] "ENSG00000128294.16 TPST2" "ENSG00000113448.19 PDE4D"
## [121] "ENSG00000237788.1 RP5-1041C10.3" "ENSG00000073737.17 DHRS9"
## [123] "ENSG00000184385.2 UMODL1-AS1" "ENSG00000115425.14 PECR"
## [125] "ENSG00000150347.17 ARID5B" "ENSG00000182541.18 LIMK2"
## [127] "ENSG00000204634.13 TBC1D8" "ENSG00000251139.2 RP11-701P16.2"
## [129] "ENSG00000249138.1 SLED1" "ENSG00000106789.13 CORO2A"
## [131] "ENSG00000261342.1 AC006538.1" "ENSG00000178342.4 KCNG2"
## [133] "ENSG00000170340.11 B3GNT2" "ENSG00000136634.7 IL10"
## [135] "ENSG00000151694.14 ADAM17" "ENSG00000044574.9 HSPA5"
```
``` r
intersect( rownames(subset(dex_eos,padj<0.05 & log2FoldChange<0)) , rownames(subset(crp_pod1,padj<0.05 & log2FoldChange<0)) )
```
```
## [1] "ENSG00000168389.18 MFSD2A" "ENSG00000130558.20 OLFM1"
## [3] "ENSG00000242574.9 HLA-DMB" "ENSG00000196664.5 TLR7"
## [5] "ENSG00000168913.7 ENHO" "ENSG00000151117.9 TMEM86A"
## [7] "ENSG00000175262.14 C1orf127" "ENSG00000154736.6 ADAMTS5"
## [9] "ENSG00000128284.19 APOL3" "ENSG00000114013.16 CD86"
## [11] "ENSG00000204257.15 HLA-DMA" "ENSG00000118257.17 NRP2"
## [13] "ENSG00000010610.10 CD4" "ENSG00000153823.19 PID1"
## [15] "ENSG00000179583.20 CIITA" "ENSG00000116990.11 MYCL"
## [17] "ENSG00000162734.13 PEA15" "ENSG00000111452.13 ADGRD1"
## [19] "ENSG00000184221.13 OLIG1" "ENSG00000157445.15 CACNA2D3"
## [21] "ENSG00000166866.13 MYO1A" "ENSG00000165795.24 NDRG2"
## [23] "ENSG00000106123.12 EPHB6" "ENSG00000055957.11 ITIH1"
## [25] "ENSG00000132846.6 ZBED3" "ENSG00000174370.11 C11orf45"
## [27] "ENSG00000213694.6 S1PR3" "ENSG00000160013.9 PTGIR"
## [29] "ENSG00000020577.14 SAMD4A" "ENSG00000181908.5 LINC02724"
## [31] "ENSG00000100095.19 SEZ6L" "ENSG00000141510.18 TP53"
## [33] "ENSG00000204219.11 TCEA3" "ENSG00000165457.14 FOLR2"
## [35] "ENSG00000231389.7 HLA-DPA1" "ENSG00000204287.14 HLA-DRA"
## [37] "ENSG00000271009.3 RP11-346C20.4" "ENSG00000143819.13 EPHX1"
## [39] "ENSG00000183780.13 SLC35F3" "ENSG00000197448.14 GSTK1"
## [41] "ENSG00000103319.12 EEF2K" "ENSG00000043514.17 TRIT1"
## [43] "ENSG00000019582.16 CD74" "ENSG00000074660.16 SCARF1"
## [45] "ENSG00000186318.18 BACE1" "ENSG00000150433.10 TMEM218"
## [47] "ENSG00000117266.16 CDK18" "ENSG00000169245.6 CXCL10"
## [49] "ENSG00000164828.18 SUN1" "ENSG00000182287.15 AP1S2"
## [51] "ENSG00000092094.11 OSGEP" "ENSG00000146409.12 SLC18B1"
## [53] "ENSG00000120896.14 SORBS3" "ENSG00000004455.17 AK2"
## [55] "ENSG00000165092.13 ALDH1A1" "ENSG00000139970.17 RTN1"
## [57] "ENSG00000130147.16 SH3BP4" "ENSG00000147130.14 ZMYM3"
## [59] "ENSG00000006062.18 MAP3K14" "ENSG00000196126.11 HLA-DRB1"
## [61] "ENSG00000107282.8 APBA1" "ENSG00000105808.18 RASA4"
## [63] "ENSG00000270001.1 RP11-218C14.8" "ENSG00000168026.19 TTC21A"
## [65] "ENSG00000196735.13 HLA-DQA1" "ENSG00000165125.22 TRPV6"
## [67] "ENSG00000111269.3 CREBL2" "ENSG00000149927.18 DOC2A"
## [69] "ENSG00000185361.9 TNFAIP8L1" "ENSG00000259436.1 CTC-378H22.2"
## [71] "ENSG00000143390.18 RFX5" "ENSG00000187017.17 ESPN"
## [73] "ENSG00000090447.12 TFAP4" "ENSG00000110811.20 P3H3"
## [75] "ENSG00000175691.9 ZNF77" "ENSG00000162139.10 NEU3"
## [77] "ENSG00000182749.6 PAQR7" "ENSG00000109790.18 KLHL5"
## [79] "ENSG00000102678.7 FGF9" "ENSG00000150627.16 WDR17"
## [81] "ENSG00000260496.3 RP11-161M6.3" "ENSG00000059588.10 TARBP1"
## [83] "ENSG00000181885.18 CLDN7" "ENSG00000186918.14 ZNF395"
## [85] "ENSG00000170275.15 CRTAP" "ENSG00000091592.16 NLRP1"
## [87] "ENSG00000005882.12 PDK2" "ENSG00000170667.15 RASA4B"
## [89] "ENSG00000167107.13 ACSF2" "ENSG00000092200.13 RPGRIP1"
## [91] "ENSG00000077232.19 DNAJC10" "ENSG00000215067.10 ALOX12-AS1"
## [93] "ENSG00000214783.9 POLR2J4" "ENSG00000179057.14 IGSF22"
## [95] "ENSG00000140931.20 CMTM3" "ENSG00000166619.15 BLCAP"
## [97] "ENSG00000011143.19 MKS1" "ENSG00000184271.17 POU6F1"
## [99] "ENSG00000116455.14 WDR77" "ENSG00000180758.12 GPR157"
## [101] "ENSG00000243335.10 KCTD7" "ENSG00000072210.19 ALDH3A2"
## [103] "ENSG00000214022.12 REPIN1" "ENSG00000151136.15 BTBD11"
## [105] "ENSG00000270012.1 LL0XNC01-7P3.1" "ENSG00000074621.14 SLC24A1"
## [107] "ENSG00000117480.16 FAAH" "ENSG00000149483.12 TMEM138"
```
``` r
intersect( rownames(subset(dex_eos,padj<0.05 & log2FoldChange>0)) , rownames(subset(crp_pod1,padj<0.05 & log2FoldChange<0)) )
```
```
## [1] "ENSG00000158485.11 CD1B" "ENSG00000179859.10 RNF227"
## [3] "ENSG00000106952.8 TNFSF8" "ENSG00000136944.19 LMX1B"
## [5] "ENSG00000205531.13 NAP1L4" "ENSG00000158488.16 CD1E"
## [7] "ENSG00000237973.1 MTCO1P12" "ENSG00000049089.15 COL9A2"
```
``` r
intersect( rownames(subset(dex_eos,padj<0.05 & log2FoldChange<0)) , rownames(subset(crp_pod1,padj<0.05 & log2FoldChange>0)) )
```
```
## [1] "ENSG00000198959.12 TGM2" "ENSG00000229436.1 AC073850.6"
## [3] "ENSG00000225370.1 AC011515.2" "ENSG00000139567.13 ACVRL1"
## [5] "ENSG00000106012.18 IQCE" "ENSG00000135218.19 CD36"
## [7] "ENSG00000159110.21 IFNAR2" "ENSG00000211891.6 IGHE"
## [9] "ENSG00000135407.10 AVIL" "ENSG00000136960.13 ENPP2"
## [11] "ENSG00000171812.13 COL8A2" "ENSG00000100376.12 FAM118A"
## [13] "ENSG00000135047.16 CTSL" "ENSG00000138119.17 MYOF"
## [15] "ENSG00000113231.14 PDE8B" "ENSG00000111199.12 TRPV4"
## [17] "ENSG00000174837.15 ADGRE1" "ENSG00000178996.14 SNX18"
## [19] "ENSG00000102524.12 TNFSF13B" "ENSG00000026508.20 CD44"
## [21] "ENSG00000007968.7 E2F2" "ENSG00000287367.1 CTD-2591A1.2"
## [23] "ENSG00000136689.19 IL1RN" "ENSG00000119321.9 FKBP15"
## [25] "ENSG00000085276.19 MECOM" "ENSG00000267676.1 THA1P"
## [27] "ENSG00000189419.8 SPATA41" "ENSG00000197632.9 SERPINB2"
## [29] "ENSG00000054967.13 RELT"
```
#### Stratified, unadjusted
* crp_t0_a
* crp_t0_b
* crp_eos_a
* crp_eos_b
* crp_pod1_a
* crp_pod1_b
* dex_crplo_t0
* dex_crphi_t0
* dex_crplo_eos
* dex_crphi_eos
* dex_crplo_pod1
* dex_crphi_pod1
``` r
l2 <- list("crp_t0_a"=crp_t0_a, "crp_t0_b"=crp_t0_b,
"crp_eos_a"=crp_eos_a, "crp_eos_b"=crp_eos_b,
"crp_pod1_a"= crp_pod1_a, "crp_pod1_b"=crp_pod1_b,
"dex_crplo_t0"=dex_crplo_t0, "dex_crphi_t0"= dex_crphi_t0,
"dex_crplo_eos"=dex_crplo_eos, "dex_crphi_eos"=dex_crphi_eos,
"dex_crplo_pod1"=dex_crplo_pod1, "dex_crphi_pod1"=dex_crphi_pod1)
lapply(1:length(l2),function(i) {
volcanoplot(x=l2[[i]], title=names(l2)[[i]])
smearplot(x=l2[[i]], title=names(l2)[[i]])
print( head(l2[[i]],50) |>
kbl(caption = paste(names(l2)[[i]],"top 50 genes")) |>
kable_paper("hover", full_width = F) )
} )
```
```
## [[1]]
##
## [[2]]
##
## [[3]]
##
## [[4]]
##
## [[5]]
##
## [[6]]
##
## [[7]]
##
## [[8]]
##
## [[9]]
##
## [[10]]
##
## [[11]]
##
## [[12]]
```
``` r
debar(l2) ; par(mar = c(5.1, 4.1, 4.1, 2.1))
```
``` r
myeuler(list("crp_t0_a"=crp_t0_a, "crp_t0_b"=crp_t0_b,"dex_crplo_t0"=dex_crplo_t0, "dex_crphi_t0"= dex_crphi_t0))
```
``` r
myeuler(list("crp_eos_a"=crp_eos_a, "crp_eos_b"=crp_eos_b,"dex_crplo_eos"=dex_crplo_eos, "dex_crphi_eos"=dex_crphi_eos))
```
``` r
myeuler(list("crp_pod1_a"= crp_pod1_a, "crp_pod1_b"=crp_pod1_b,"dex_crplo_pod1"=dex_crplo_pod1, "dex_crphi_pod1"=dex_crphi_pod1))
```
``` r
message("crp_t0_a")
```
```
## crp_t0_a
```
``` r
datatable(crp_t0_a[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_t0_b")
```
```
## crp_t0_b
```
``` r
datatable(crp_t0_b[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_eos_a")
```
```
## crp_eos_a
```
``` r
datatable(crp_eos_a[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_eos_b")
```
```
## crp_eos_b
```
``` r
datatable(crp_eos_b[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_pod1_a")
```
```
## crp_pod1_a
```
``` r
datatable(crp_pod1_a[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_pod1_b")
```
```
## crp_pod1_b
```
``` r
datatable(crp_pod1_b[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crplo_t0")
```
```
## dex_crplo_t0
```
``` r
datatable(dex_crplo_t0[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crphi_t0")
```
```
## dex_crphi_t0
```
``` r
datatable(dex_crphi_t0[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crplo_eos")
```
```
## dex_crplo_eos
```
``` r
datatable(dex_crplo_eos[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crphi_eos")
```
```
## dex_crphi_eos
```
``` r
datatable(dex_crphi_eos[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crplo_pod1")
```
```
## dex_crplo_pod1
```
``` r
datatable(dex_crplo_pod1[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crphi_pod1")
```
```
## dex_crphi_pod1
```
``` r
datatable(dex_crphi_pod1[1:1000,1:6])
```
```{=html}
```
### Adjusted for clinical covariates
#### Unstratified, adjusted
* crp_t0_adj
* crp_eos_adj
* crp_pod1_adj
* dex_t0_adj
* dex_eos_adj
* dex_pod1_adj
``` r
l3 <- list("crp_t0_adj"=crp_t0_adj, "crp_eos_adj"=crp_eos_adj, "crp_pod1_adj"=crp_pod1_adj,
"dex_t0_adj"=dex_t0_adj,"dex_eos_adj"=dex_eos_adj,"dex_pod1_adj"=dex_pod1_adj )
lapply(1:length(l3),function(i) {
volcanoplot(x=l3[[i]], title=names(l3)[[i]])
smearplot(x=l3[[i]], title=names(l3)[[i]])
print( head(l1[[i]],50) |>
kbl(caption = paste(names(l3)[[i]],"top 50 genes")) |>
kable_paper("hover", full_width = F) )
} )
```
```
## [[1]]
##
## [[2]]
##
## [[3]]
##
## [[4]]
##
## [[5]]
##
## [[6]]
```
``` r
debar(l3) ; par(mar = c(5.1, 4.1, 4.1, 2.1))
```
``` r
myeuler(list("crp_t0_adj"=crp_t0_adj,"crp_eos_adj"=crp_eos_adj))
```
``` r
myeuler(list("crp_eos_adj"=crp_eos_adj,"crp_pod1_adj"=crp_pod1_adj))
```
``` r
myeuler(list("dex_t0_adj"=dex_t0_adj,"dex_eos_adj"=dex_eos_adj))
```
``` r
myeuler(list("dex_eos_adj"=dex_eos_adj,"dex_pod1_adj"=dex_pod1_adj))
```
``` r
myeuler(list("crp_t0_adj"=crp_t0_adj,"dex_t0_adj"=dex_t0_adj))
```
``` r
myeuler(list("crp_eos_adj"=crp_eos_adj,"dex_eos_adj"=dex_eos_adj))
```
``` r
myeuler(list("crp_pod1_adj"=crp_pod1_adj,"dex_pod1_adj"=dex_pod1_adj))
```
``` r
myeuler(list("crp_pod1_adj"=crp_pod1_adj,"dex_eos_adj"=dex_eos_adj))
```
``` r
message("crp_t0_adj")
```
```
## crp_t0_adj
```
``` r
datatable(crp_t0_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_eos_adj")
```
```
## crp_eos_adj
```
``` r
datatable(crp_eos_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_pod1_adj")
```
```
## crp_pod1_adj
```
``` r
datatable(crp_pod1_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_t0_adj")
```
```
## dex_t0_adj
```
``` r
datatable(dex_t0_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_eos_adj")
```
```
## dex_eos_adj
```
``` r
datatable(dex_eos_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_pod1_adj")
```
```
## dex_pod1_adj
```
``` r
datatable(dex_pod1_adj[1:1000,1:6])
```
```{=html}
```
#### Stratified, adjusted
* crp_t0_a_adj
* crp_t0_b_adj
* crp_eos_a_adj
* crp_eos_b_adj
* crp_pod1_a_adj
* crp_pod1_b_adj
* dex_crplo_t0_adj
* dex_crphi_t0_adj
* dex_crplo_eos_adj
* dex_crphi_eos_adj
* dex_crplo_pod1_adj
* dex_crphi_pod1_adj
``` r
l4 <- list("crp_t0_a_adj"=crp_t0_a_adj, "crp_t0_b_adj"=crp_t0_b_adj,
"crp_eos_a_adj"=crp_eos_a_adj, "crp_eos_b_adj"=crp_eos_b_adj,
"crp_pod1_a_adj"= crp_pod1_a_adj, "crp_pod1_b_adj"=crp_pod1_b_adj,
"dex_crplo_t0_adj"=dex_crplo_t0_adj, "dex_crphi_t0_adj"=dex_crphi_t0_adj,
"dex_crplo_eos_adj"=dex_crplo_eos_adj, "dex_crphi_eos_adj"=dex_crphi_eos_adj,
"dex_crplo_pod1_adj"=dex_crplo_pod1_adj, "dex_crphi_pod1_adj"=dex_crphi_pod1_adj)
lapply(1:length(l4),function(i) {
volcanoplot(x=l2[[i]], title=names(l2)[[i]])
smearplot(x=l2[[i]], title=names(l2)[[i]])
print( head(l2[[i]],50) |>
kbl(caption = paste(names(l2)[[i]],"top 50 genes")) |>
kable_paper("hover", full_width = F) )
} )
```
```
## [[1]]
##
## [[2]]
##
## [[3]]
##
## [[4]]
##
## [[5]]
##
## [[6]]
##
## [[7]]
##
## [[8]]
##
## [[9]]
##
## [[10]]
##
## [[11]]
##
## [[12]]
```
``` r
debar(l4) ; par(mar = c(5.1, 4.1, 4.1, 2.1))
```
``` r
myeuler(list("crp_t0_a_adj"=crp_t0_a_adj, "crp_t0_b_adj"=crp_t0_b_adj,
"dex_crplo_t0_adj"=dex_crplo_t0_adj, "dex_crphi_t0_adj"= dex_crphi_t0_adj))
```
``` r
myeuler(list("crp_eos_a_adj"=crp_eos_a_adj, "crp_eos_b_adj"=crp_eos_b_adj,
"dex_crplo_eos_adj"=dex_crplo_eos_adj, "dex_crphi_eos_adj"=dex_crphi_eos_adj))
```
``` r
myeuler(list("crp_pod1_a_adj"= crp_pod1_a_adj, "crp_pod1_b_adj"=crp_pod1_b_adj,
"dex_crplo_pod1_adj"=dex_crplo_pod1_adj, "dex_crphi_pod1_adj"=dex_crphi_pod1_adj))
```
``` r
message("crp_t0_a_adj")
```
```
## crp_t0_a_adj
```
``` r
datatable(crp_t0_a_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_t0_b_adj")
```
```
## crp_t0_b_adj
```
``` r
datatable(crp_t0_b_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_eos_a_adj")
```
```
## crp_eos_a_adj
```
``` r
datatable(crp_eos_a_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_eos_b_adj")
```
```
## crp_eos_b_adj
```
``` r
datatable(crp_eos_b_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_pod1_a_adj")
```
```
## crp_pod1_a_adj
```
``` r
datatable(crp_pod1_a_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("crp_pod1_b_adj")
```
```
## crp_pod1_b_adj
```
``` r
datatable(crp_pod1_b_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crplo_t0_adj")
```
```
## dex_crplo_t0_adj
```
``` r
datatable(dex_crplo_t0_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crphi_t0_adj")
```
```
## dex_crphi_t0_adj
```
``` r
datatable(dex_crphi_t0_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crplo_eos_adj")
```
```
## dex_crplo_eos_adj
```
``` r
datatable(dex_crplo_eos_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crphi_eos_adj")
```
```
## dex_crphi_eos_adj
```
``` r
datatable(dex_crphi_eos_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crplo_pod1_adj")
```
```
## dex_crplo_pod1_adj
```
``` r
datatable(dex_crplo_pod1_adj[1:1000,1:6])
```
```{=html}
```
``` r
message("dex_crphi_pod1_adj")
```
```
## dex_crphi_pod1_adj
```
``` r
datatable(dex_crphi_pod1_adj[1:1000,1:6])
```
```{=html}
```
## Save data
``` r
writeTSV(l1)
```
```
## [[1]]
## NULL
##
## [[2]]
## NULL
##
## [[3]]
## NULL
##
## [[4]]
## NULL
##
## [[5]]
## NULL
##
## [[6]]
## NULL
```
``` r
writeTSV(l2)
```
```
## [[1]]
## NULL
##
## [[2]]
## NULL
##
## [[3]]
## NULL
##
## [[4]]
## NULL
##
## [[5]]
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## [[8]]
## NULL
##
## [[9]]
## NULL
##
## [[10]]
## NULL
##
## [[11]]
## NULL
##
## [[12]]
## NULL
```
``` r
writeTSV(l3)
```
```
## [[1]]
## NULL
##
## [[2]]
## NULL
##
## [[3]]
## NULL
##
## [[4]]
## NULL
##
## [[5]]
## NULL
##
## [[6]]
## NULL
```
``` r
writeTSV(l4)
```
```
## [[1]]
## NULL
##
## [[2]]
## NULL
##
## [[3]]
## NULL
##
## [[4]]
## NULL
##
## [[5]]
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## NULL
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## NULL
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## NULL
##
## [[11]]
## NULL
##
## [[12]]
## NULL
```
``` r
system('sed -i "s#^baseMean#GeneID\tbaseMean#" *tsv')
```
## Session information
For reproducibility
``` r
sessionInfo()
```
```
## R version 4.5.2 (2025-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
## [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] RhpcBLASctl_0.23-42 xlsx_0.6.5
## [3] DT_0.34.0 eulerr_7.1.0
## [5] ggplot2_4.0.3 kableExtra_1.4.0
## [7] MASS_7.3-65 mitch_1.22.1
## [9] DESeq2_1.50.2 SummarizedExperiment_1.40.0
## [11] Biobase_2.70.0 MatrixGenerics_1.22.0
## [13] matrixStats_1.5.0 GenomicRanges_1.62.1
## [15] Seqinfo_1.0.0 IRanges_2.44.0
## [17] S4Vectors_0.48.1 BiocGenerics_0.56.0
## [19] generics_0.1.4 dplyr_1.2.1
## [21] WGCNA_1.74 fastcluster_1.3.0
## [23] dynamicTreeCut_1.63-1 reshape2_1.4.5
## [25] gplots_3.3.0
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-9 gridExtra_2.3 echarts4r_0.5.0
## [4] rlang_1.2.0 magrittr_2.0.4 otel_0.2.0
## [7] compiler_4.5.2 polylabelr_1.0.0 systemfonts_1.3.1
## [10] vctrs_0.7.3 stringr_1.6.0 pkgconfig_2.0.3
## [13] fastmap_1.2.0 backports_1.5.1 XVector_0.50.0
## [16] caTools_1.18.3 promises_1.5.0 rmarkdown_2.30
## [19] preprocessCore_1.72.0 network_1.20.0 purrr_1.2.0
## [22] xfun_0.54 cachem_1.1.0 jsonlite_2.0.0
## [25] later_1.4.4 DelayedArray_0.36.1 xlsxjars_0.9.0
## [28] BiocParallel_1.44.0 parallel_4.5.2 cluster_2.1.8.1
## [31] R6_2.6.1 bslib_0.9.0 stringi_1.8.7
## [34] RColorBrewer_1.1-3 GGally_2.4.0 rpart_4.1.24
## [37] jquerylib_0.1.4 Rcpp_1.1.1-1.1 iterators_1.0.14
## [40] knitr_1.50 base64enc_0.1-3 httpuv_1.6.16
## [43] Matrix_1.7-4 splines_4.5.2 nnet_7.3-20
## [46] tidyselect_1.2.1 rstudioapi_0.17.1 abind_1.4-8
## [49] yaml_2.3.11 doParallel_1.0.17 codetools_0.2-20
## [52] lattice_0.22-7 tibble_3.3.0 plyr_1.8.9
## [55] withr_3.0.2 shiny_1.11.1 S7_0.2.2
## [58] coda_0.19-4.1 evaluate_1.0.5 foreign_0.8-90
## [61] survival_3.8-3 polyclip_1.10-7 rJava_1.0-18
## [64] ggstats_0.13.0 xml2_1.5.1 pillar_1.11.1
## [67] KernSmooth_2.23-26 checkmate_2.3.4 foreach_1.5.2
## [70] scales_1.4.0 xtable_1.8-4 gtools_3.9.5
## [73] glue_1.8.0 Hmisc_5.2-5 tools_4.5.2
## [76] data.table_1.18.4 locfit_1.5-9.12 grid_4.5.2
## [79] impute_1.84.0 tidyr_1.3.2 crosstalk_1.2.2
## [82] colorspace_2.1-2 beeswarm_0.4.0 htmlTable_2.5.0
## [85] Formula_1.2-5 cli_3.6.5 textshaping_1.0.4
## [88] viridisLite_0.4.3 S4Arrays_1.10.1 svglite_2.2.2
## [91] gtable_0.3.6 sass_0.4.10 digest_0.6.39
## [94] SparseArray_1.10.10 htmlwidgets_1.6.4 farver_2.1.2
## [97] htmltools_0.5.8.1 lifecycle_1.0.5 statnet.common_4.13.0
## [100] mime_0.13
```