Last updated: 2020-07-23

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Knit directory: Comparative_APA/analysis/

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Unstaged changes:
    Modified:   analysis/DeandNumPAS.Rmd
    Modified:   analysis/DirSelectionKhan.Rmd
    Modified:   analysis/ExploredAPA.Rmd
    Modified:   analysis/ExploredAPA_DF.Rmd
    Modified:   analysis/MMExpreiment.Rmd
    Modified:   analysis/OppositeMap.Rmd
    Modified:   analysis/PTM_analysis.Rmd
    Modified:   analysis/ResultsNoUnlifted.Rmd
    Modified:   analysis/TotalDomStructure.Rmd
    Modified:   analysis/TotalVNuclearBothSpecies.Rmd
    Modified:   analysis/TryTripSeqAnalysis.Rmd
    Modified:   analysis/annotationInfo.Rmd
    Modified:   analysis/changeMisprimcut.Rmd
    Modified:   analysis/comp2apaQTLPAS.Rmd
    Modified:   analysis/correlationPhenos.Rmd
    Modified:   analysis/dInforContent.Rmd
    Modified:   analysis/df_QC.Rmd
    Modified:   analysis/diffExpression.Rmd
    Modified:   analysis/establishCutoffs.Rmd
    Modified:   analysis/incorporateQTLsAncestral.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/investigatePantro5.Rmd
    Modified:   analysis/mRNADecay.Rmd
    Modified:   analysis/miRNAanalysis.Rmd
    Modified:   analysis/multiMap.Rmd
    Modified:   analysis/phastCon.Rmd
    Modified:   analysis/pol2.Rmd
    Modified:   analysis/speciesSpecific.Rmd

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library(tidyverse)
── Attaching packages ───────────────────────────────────────────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.2.1     ✔ purrr   0.3.4
✔ tibble  2.1.3     ✔ dplyr   0.8.3
✔ tidyr   1.1.0     ✔ stringr 1.4.0
✔ readr   1.3.1     ✔ forcats 0.4.0
── Conflicts ──────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
library(UpSetR)
library(ggpubr)

Upload:

Protein=read.table("../data/Khan_prot/HC_SigProtein.txt", header = T, stringsAsFactors = F)%>% dplyr::rename("gene"=gene.symbol)
nameID=read.table("../../genome_anotation_data/ensemble_to_genename.txt",sep="\t", header = T, stringsAsFactors = F)
DEgenes=read.table("../data/DiffExpression/DE_genes.txt", header = F,col.names = c("Gene_stable_ID"),stringsAsFactors = F) %>% inner_join(nameID, by="Gene_stable_ID") %>% dplyr::select(Gene.name) %>% dplyr::rename("gene"=Gene.name)
NucAPA=read.table("../data/DiffIso_Nuclear_DF/SignifianceEitherGENES_Nuclear.txt",header = T,stringsAsFactors = F)

I will do this first with these then I can start to look at it by significance.

apatested=read.table("../data/DiffIso_Nuclear_DF/AllPAS_withGeneSig.txt", header = T) %>% select(gene) %>% unique()
pnotE=Protein %>% anti_join(DEgenes,by="gene") 
nrow(pnotE)
[1] 725
nrow(Protein)
[1] 1262
nrow(DEgenes)
[1] 3794
apatested %>% inner_join(pnotE,by="gene") %>% nrow()
Warning: Column `gene` joining factor and character vector, coercing into
character vector
[1] 506
APAandPnotE= NucAPA %>% inner_join(Protein, by="gene") %>% anti_join(DEgenes,by="gene")
listInput_nucOnly <- list(DE=DEgenes$gene, DAPA=NucAPA$gene, DP=Protein$gene)

#upset(fromList(listInput_nosplice), queries = list(list(query=intersects, params=list("DAPA", "DT", "DP"), color="red", active=T,query.name="APA, Ribo, Protein"),list(query=intersects, params=list("DE", "DT", "DP"), color="orange", active=T, query.name="Expression,Ribo, Protein"),list(query=intersects, params=list("DAPA", "DT"), color="blue", active=T, query.name="APA,Ribo") ,list(query=intersects, params=list("DAPA", "DP"), color="purple", active=T, query.name="APA, Protein"),list(query=intersects, params=list("DAPA", "DE"), color="green", active=T, query.name="APA, Expression")), order.by = "freq", query.legend = "bottom")




upset(fromList(listInput_nucOnly), order.by = "freq", keep.order = T,empty.intersections = "on", queries = list(list(query=intersects, params=list("DAPA", "DP"), color="darkorchid4", active=T,query.name="APA, Protein")))

90 of these genes.

Learn about these genes.

Selection:

model.num.rna: : 1 = mRNA expression level pattern consistent with directional selection along human lineage, 2 = mRNA expression level pattern consistent with directional selection along chimpanzee lineage, 3 = undetermined pattern, 4 = patterns with no significant difference between mean expression levels; 5 = evidence for relaxation of constraint along human lineage, 6 = evidence of relaxation of constraint along chimpanzee lineage

model.num.protein: 1 = protein expression level pattern consistent with directional selection along human lineage, 2 = protein expression level pattern consistent with directional selection along chimpanzee lineage, 3 = undetermined pattern, 4 = patterns with no significant difference between mean expression levels; 5 = evidence for relaxation of constraint along human lineage, 6 = evidence of relaxation of constraint along chimpanzee lineage

KhanData=read.csv("../data/Khan_prot/Khan_TableS4.csv",stringsAsFactors = F)  %>% dplyr::select(gene.symbol,contains("model") ) %>% dplyr::rename("gene"=gene.symbol, "Protein"=model.num.protein, "RNA"=model.num.rna)


APAandPnotE_sel= APAandPnotE %>% inner_join(KhanData,by="gene")

Plot the information about the RNA and protein for these:

APAandPnotE_sel_g=APAandPnotE_sel %>% dplyr::select(gene, Protein, RNA) %>% gather("Set", "Model", -gene)


APAandPnotE_sel_g$Model= as.factor(APAandPnotE_sel_g$Model)
ggplot(APAandPnotE_sel_g,aes(x=Model, by=Set, fill=Set)) + geom_bar(stat="count", position="dodge") + scale_fill_brewer(palette = "RdYlBu")

Version Author Date
1de69e8 brimittleman 2020-07-03
6d8725a brimittleman 2020-04-10
c2a0778 brimittleman 2020-04-06
25a4790 brimittleman 2020-03-07

Plot protein only:

APAandPnotE_sel_gOnlyP= APAandPnotE_sel_g %>% filter(Set=="Protein")

APAandPnotE_sel_gOnlyP$Model= as.factor(APAandPnotE_sel_gOnlyP$Model)

ggplot(APAandPnotE_sel_gOnlyP,aes(x=Model)) + geom_bar(stat="count", position="dodge", fill="darkorchid4") + labs(y="Number of Genes", x="Protein Selection Model", title="Protein and APA differences\n no difference in Expression") + scale_x_discrete( labels=c("Selection Human","Selection Chimp","Undetermined","No mean difference","Relaxation in Chimp"))+theme(axis.text.x=element_text(angle=90, hjust=0), text= element_text(size=16)) 

The genes in 1,2,5,6 are interesting.

APAandPnotE_selCalled= APAandPnotE_sel_g %>% filter(Set=="Protein", Model %in% c(1,2,5,6))

There are 20 of these genes:

APAandPnotE_selCalled
      gene     Set Model
1     RRM1 Protein     1
2    SART3 Protein     1
3    SUGT1 Protein     2
4    VPS36 Protein     1
5  ATP6V1D Protein     1
6   GALNT2 Protein     2
7    GNAI3 Protein     2
8   SEC22B Protein     2
9    WDR77 Protein     2
10    KYNU Protein     2
11   PPIL3 Protein     1
12    CPOX Protein     2
13   MANBA Protein     1
14   BNIP1 Protein     1
15    CCT5 Protein     2
16  CYFIP2 Protein     1
17    MYO6 Protein     2
18    CUL1 Protein     2
19   VPS41 Protein     1
20    STOM Protein     1

Where are the differential PAS in these genes:

#APAandPnotE_sel_gOnlyP
Meta=read.table("../data/PAS_doubleFilter/PAS_5perc_either_HumanCoord_BothUsage_meta_doubleFilter.txt", header = T, stringsAsFactors = T) %>% dplyr::rename("ChimpUsage"=Chimp, "HumanUsage"=Human)
NucAPAres=read.table("../data/DiffIso_Nuclear_DF/AllPAS_withGeneSig.txt", header = T,stringsAsFactors = F) %>% inner_join(Meta, by=c("chr", "start","end", "gene"))
Warning: Column `chr` joining character vector and factor, coercing into
character vector
Warning: Column `gene` joining character vector and factor, coercing into
character vector
NucAPAres_DP= NucAPAres %>% filter(gene %in%APAandPnotE_sel_gOnlyP$gene ) %>% filter(SigPAU2=="Yes")


NucAPAresSig=NucAPAres %>% filter(SigPAU2=="Yes")

THere are 154 PAS in this set:

ggplot(NucAPAres_DP,aes(x=loc,fill=loc))+ geom_bar(stat="count") + scale_fill_brewer(palette = "RdYlBu")+theme(axis.text.x=element_text(angle=90, hjust=0), text= element_text(size=16), legend.position = "false") + labs(x="", y="Number of PAS", title="Expression independent PAS locations")

Version Author Date
1de69e8 brimittleman 2020-07-03
961b808 brimittleman 2020-04-23
5d82297 brimittleman 2020-04-22
6d8725a brimittleman 2020-04-10
c2a0778 brimittleman 2020-04-06
25a4790 brimittleman 2020-03-07

Enrichment for this:

Compare to all of the significant in that location.

NucAPAres_sig= NucAPAres %>% filter(SigPAU2=="Yes") %>% mutate(dPnotE=ifelse(PAS %in% NucAPAres_DP$PAS,"Yes", "No"))


enrich=c()
pval=c()

for (i in c("cds", "end", "intron", "utr3")){
  x=nrow(NucAPAres_sig %>% filter(dPnotE=="Yes", loc==i))
  m=nrow(NucAPAres_sig %>% filter( loc==i))
  n=nrow(NucAPAres_sig %>% filter(loc!=i))
  k=nrow(NucAPAres_sig %>% filter(dPnotE=="Yes"))
  N=nrow(NucAPAres_sig)
  pval=c(pval, phyper(x-1,m,n,k,lower.tail=F))
  enrichval=(x/k)/(m/N)
  enrich=c(enrich, enrichval)
}
enrich
[1] 1.3100158 0.3521451 0.7012860 1.2145339
pval
[1] 0.144079246 0.993503594 0.976950002 0.005705065
NucAPAres_DPLocEnrich=NucAPAres_DP %>% group_by(loc) %>% summarise(n=n()) %>% bind_cols(enrichment=enrich, pvalue=pval)


locplot=ggplot(NucAPAres_DPLocEnrich, aes(x=loc, y=n, fill=loc)) + geom_bar(stat="identity") + scale_fill_brewer(palette = "RdYlBu")+theme(axis.text.x=element_text(angle=90, hjust=0), text= element_text(size=16), legend.position = "false") + labs(x="", y="Number of PAS", title="Expression independent PAS locations")+ geom_text(aes(label=paste("Enrichment=",round(enrichment,2), "X", sep=""), vjust=0)) +geom_text(aes(label=paste("Pval=",round(pvalue,3), sep=""), vjust=2))+ theme_classic() +  theme(legend.position = "none", axis.text.x = element_text(size=10),plot.title = element_text(hjust = 0.5, face="bold"),axis.text.y = element_text(size=10),text=element_text(size=10),plot.margin = unit(c(0,0,0,0), "cm"))
locplot

Version Author Date
1de69e8 brimittleman 2020-07-03
961b808 brimittleman 2020-04-23
3790efa brimittleman 2020-04-23
5d82297 brimittleman 2020-04-22
6d8725a brimittleman 2020-04-10
c2a0778 brimittleman 2020-04-06
25a4790 brimittleman 2020-03-07

Interactions:

Are there differences in protien interactions for these.

Interactions=read.table("../data/bioGRID/GeneswInteractions.txt",stringsAsFactors = F, header = T) 

OrthoUTR=read.table("../data/orthoUTR/HumanDistal3UTR.sort.bed", col.names = c("chr",'start','end','gene','score','strand'),stringsAsFactors = F) %>% mutate(length=end-start) %>% select(gene, length)


InteractionsAPA=Interactions %>%filter(gene %in% NucAPAresSig$gene) %>% mutate(dPnotE=ifelse(gene %in% NucAPAres_DP$gene, "Yes", "No"))%>% inner_join(OrthoUTR, by="gene") %>% mutate(density=nInt/length)


ggplot(InteractionsAPA,aes(x=dPnotE, y=log10(nInt+1),fill=dPnotE)) + geom_boxplot(notch = T) + stat_compare_means() + scale_fill_brewer(palette = "Set1")+theme(axis.text.x=element_text(angle=90, hjust=0), text= element_text(size=16), legend.position = "false") + labs(x="Gene in Expression independent set", y="log10(Number of Protein Interactions)", title="Protein Interactions for Expression \nindependent dAPA genes")

Version Author Date
1de69e8 brimittleman 2020-07-03

Plot density?

ggplot(InteractionsAPA,aes(x=dPnotE, y=log10(density),fill=dPnotE)) + geom_boxplot(notch = T) + stat_compare_means() + scale_fill_brewer(palette = "Set1")+theme(axis.text.x=element_text(angle=90, hjust=0), text= element_text(size=16), legend.position = "false") + labs(x="Gene in Expression independent set", y="log10(UTR density of interactions)", title="Protein Interactions for Expression \nindependent dAPA genes")

Version Author Date
961b808 brimittleman 2020-04-23
5d82297 brimittleman 2020-04-22
6d8725a brimittleman 2020-04-10
c2a0778 brimittleman 2020-04-06
25a4790 brimittleman 2020-03-07

More likly to have one:

InteractionsAPA %>% mutate(HasInteraction=ifelse(nInt>0, "Yes", "No")) %>% group_by(dPnotE, HasInteraction) %>% summarise(nWithSet=n())
# A tibble: 2 x 3
# Groups:   dPnotE [2]
  dPnotE HasInteraction nWithSet
  <chr>  <chr>             <int>
1 No     Yes                1292
2 Yes    Yes                  86

Set should be the interaction set dAPA, de, and dP.

Alldiff=Protein %>% inner_join(DEgenes,by="gene") %>% inner_join(NucAPA, by="gene") %>% dplyr::select(gene)
#This is 101 genes.  
geneAPAPnotEG=APAandPnotE %>% dplyr::select(gene)

GenesMatter= Alldiff %>% bind_rows(geneAPAPnotEG) %>% mutate(Ex=ifelse(gene %in% geneAPAPnotEG$gene, "No", "Yes")) %>% inner_join(Interactions, by="gene")
ggplot(GenesMatter, aes(x=Ex, y=nInt, fill=Ex))+ geom_boxplot() + stat_compare_means() + scale_fill_brewer(palette = "RdYlBu")+theme(axis.text.x=element_text(angle=90, hjust=0), text= element_text(size=16), legend.position = "false") + labs(x="DE gene", y="Number of protein protein interactions", title="dAPA, DP, and DE")

Version Author Date
1de69e8 brimittleman 2020-07-03
961b808 brimittleman 2020-04-23

Effect sizes :

Look at the PAS effect sizes here and in protien, translation, and expression.

NucAPAres_sig_dpnotE = NucAPAres_sig %>% filter(dPnotE =="Yes")

#nameID=read.table("../../genome_anotation_data/ensemble_to_genename.txt",sep="\t", header = T, stringsAsFactors = F) %>% dplyr::select(Gene_stable_ID, Gene.name)
#DE data
DE=read.table("../data/DiffExpression/DEtested_allres.txt",stringsAsFactors = F,header = F, col.names = c("Gene_stable_ID" ,"logFC" ,"AveExpr" , "t" ,  "P.Value" ,  "adj.P.Val", "B"  )) %>% inner_join(nameID,by="Gene_stable_ID") %>% dplyr::rename('gene'=Gene.name) %>% dplyr::select(-Gene_stable_ID)
#translation
Ribo=read.table("../data/Wang_ribo/Additionaltable5_translationComparisons.txt",header = T, stringsAsFactors = F) %>% dplyr::rename("Gene_stable_ID"= ENSG) %>% inner_join(nameID,by="Gene_stable_ID") %>% dplyr::select(Gene.name, HvC.beta, HvC.pvalue, HvC.FDR) %>% dplyr::rename("gene"=Gene.name)
#prot  
Prot=read.table("../data/Khan_prot/ProtData_effectSize.txt", header = T, stringsAsFactors = F)
APAandE=NucAPAres_sig_dpnotE %>% inner_join(DE, by="gene")

ggplot(APAandE, aes(x=logFC, y=deltaPAU)) + geom_point(alpha=.3) + geom_smooth(method="lm") +stat_cor()

ggplot(APAandE, aes(x=logFC, y=deltaPAU, col=loc)) + geom_point(alpha=.3) + geom_smooth(method="lm")  +stat_cor(label.x = 1)

APAandRibo=NucAPAres_sig_dpnotE %>% inner_join(Ribo, by="gene")
ggplot(APAandRibo, aes(x=HvC.beta, y=deltaPAU)) + geom_point(alpha=.3) + geom_smooth(method="lm") +stat_cor()

APAandprot=NucAPAres_sig_dpnotE %>% inner_join(Prot, by="gene")

ggplot(APAandprot, aes(x=logEf, y=deltaPAU))+ geom_point(alpha=.3) + geom_smooth(method="lm") +stat_cor( )

ggplot(APAandprot, aes(x=logEf, y=deltaPAU, col=loc))+ geom_point(alpha=.3) + geom_smooth(method="lm") +stat_cor( )

None of these are significant.

Check if any of these are genes with QTLs.

I will pull in the genes with nuclear apaQTLs first.

apaQTLs=read.table("../../apaQTL/data/apaQTLs/Nuclear_apaQTLs4pc_5fdr.sort.bed",col.names = c('chr','start','end', 'PASid','score', 'strand')) %>% separate(PASid, into=c("gene", "PAS", "loc"),sep=":")

apaQTLGenes= apaQTLs %>% select(gene) %>% unique()
APAandPnotE_apaQTL=APAandPnotE %>% mutate(apaQTL=ifelse(gene %in% apaQTLGenes$gene, "Yes", "No"))


APAandPnotE_apaQTL %>% group_by(apaQTL) %>% summarize(n=n())
# A tibble: 2 x 2
  apaQTL     n
  <chr>  <int>
1 No        86
2 Yes        4
APAandPnotE_apaQTL %>% filter(apaQTL=="Yes")
    gene HC.qvalues.protein            ENSG apaQTL
1  STAT6        0.049128043 ENSG00000166888    Yes
2  RHOT1        0.009672323 ENSG00000126858    Yes
3 RNASEL        0.006755528 ENSG00000135828    Yes
4  BNIP1        0.021646516 ENSG00000113734    Yes

Background for enrichment is all of the dAPA genes.

x= nrow(APAandPnotE_apaQTL %>% filter(apaQTL =="Yes"))
m= nrow(APAandPnotE_apaQTL)
n=nrow(NucAPA)- nrow(APAandPnotE_apaQTL)
k=nrow(apaQTLGenes)
x
[1] 4
#expected
which(grepl(max(dhyper(1:x, m, n, k)), dhyper(1:x, m, n, k)))
[1] 4
phyper(x,m, n , k,lower.tail=F)
[1] 1

Not enriched for apaQTL.

pQTLs

Using protien specific QTLs from Battle et al.

pQTLs=read.table("../../apaQTL/data/Battle_pQTL/psQTLGeneNames.txt")

APAandPnotE_pQTL=APAandPnotE %>% mutate(pQTL=ifelse(gene %in% pQTLs$V1, "Yes", "No"))


APAandPnotE_pQTL %>% group_by(pQTL) %>% summarize(n=n())
# A tibble: 2 x 2
  pQTL      n
  <chr> <int>
1 No       86
2 Yes       4
APAandPnotE_pQTL %>% filter(pQTL=="Yes")
     gene HC.qvalues.protein            ENSG pQTL
1   TARS2        0.004796093 ENSG00000143374  Yes
2 ZBTB8OS        0.000021900 ENSG00000176261  Yes
3   NUP50        0.002061087 ENSG00000093000  Yes
4    UBA6        0.000154285 ENSG00000033178  Yes
x= nrow(APAandPnotE_pQTL %>% filter(pQTL =="Yes"))
m= nrow(APAandPnotE_pQTL)
n=nrow(NucAPA)- nrow(APAandPnotE_pQTL)
k=nrow(pQTLs)
x
[1] 4
#expected
which(grepl(max(dhyper(1:x, m, n, k)), dhyper(1:x, m, n, k)))
[1] 4
phyper(x,m, n , k,lower.tail=F)
[1] 0.8959063

Are any of the these the diff dom set? Test .4 first:

HumanRes=read.table("../data/DomDefGreaterX/Human_AllGenes_DiffTop.txt", col.names = c("Human_PAS", "gene","Human_DiffDom"),stringsAsFactors = F)

ChimpRes=read.table("../data/DomDefGreaterX/Chimp_AllGenes_DiffTop.txt", col.names = c("Chimp_PAS", "gene","Chimp_DiffDom"),stringsAsFactors = F)

BothRes=HumanRes %>% inner_join(ChimpRes,by="gene")

BothRes_40=BothRes %>% filter(Chimp_DiffDom >=0.4 | Human_DiffDom>=0.4) %>% mutate(Set= ifelse(Human_PAS==Chimp_PAS,"Same", "Different"),cut=40)


NucAPAres_sig_sm= NucAPAres_sig %>% filter(dPnotE=="Yes")
BothRes_40_dp= BothRes_40 %>% filter(gene %in% NucAPAres_sig_sm$gene)


BothRes_40_dp %>% group_by(Set) %>% summarise(n())
# A tibble: 2 x 2
  Set       `n()`
  <chr>     <int>
1 Different     8
2 Same         32
metaSm= Meta %>% select(loc, PAS)
DiffHuman= BothRes_40_dp %>% filter(Set=="Different") %>% select(gene, Human_PAS)  %>% rename(PAS= Human_PAS)%>% inner_join(metaSm, by="PAS")
Warning: Column `PAS` joining character vector and factor, coercing into
character vector
DiffChimp= BothRes_40_dp %>% filter(Set=="Different") %>% select(gene, Chimp_PAS)%>% rename(PAS= Chimp_PAS)%>% inner_join(metaSm, by="PAS")
Warning: Column `PAS` joining character vector and factor, coercing into
character vector
DiffHuman
     gene         PAS    loc
1  SEC22B  human18938    end
2  EIF4G2  human54877   utr3
3 TUBGCP3 human100208 intron
4    IRF3 human170101   utr3
5     HK2 human183666 intron
6   PPIL3 chimp195902 intron
7    FLNB human233016   utr3
8    CPOX human235691   utr3
DiffChimp
     gene         PAS  loc
1  SEC22B  chimp17094  end
2  EIF4G2  human54890  cds
3 TUBGCP3  chimp91832 utr3
4    IRF3 human170093 utr3
5     HK2 human183677 utr3
6   PPIL3 human199028 utr3
7    FLNB human233019 utr3
8    CPOX human235678 utr3

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] 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=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] ggpubr_0.3.0    UpSetR_1.4.0    forcats_0.4.0   stringr_1.4.0  
 [5] dplyr_0.8.3     purrr_0.3.4     readr_1.3.1     tidyr_1.1.0    
 [9] tibble_2.1.3    ggplot2_3.2.1   tidyverse_1.3.0

loaded via a namespace (and not attached):
 [1] httr_1.4.1         jsonlite_1.6       carData_3.0-2     
 [4] modelr_0.1.8       assertthat_0.2.1   cellranger_1.1.0  
 [7] yaml_2.2.0         pillar_1.4.2       backports_1.1.4   
[10] lattice_0.20-38    glue_1.3.1         digest_0.6.20     
[13] RColorBrewer_1.1-2 promises_1.0.1     ggsignif_0.5.0    
[16] rvest_0.3.5        colorspace_1.4-1   htmltools_0.3.6   
[19] httpuv_1.5.1       plyr_1.8.4         pkgconfig_2.0.2   
[22] broom_0.5.2        haven_2.3.1        scales_1.1.0      
[25] whisker_0.3-2      openxlsx_4.1.0.1   later_0.8.0       
[28] rio_0.5.16         git2r_0.26.1       generics_0.0.2    
[31] farver_2.0.1       car_3.0-5          ellipsis_0.2.0.1  
[34] withr_2.1.2        lazyeval_0.2.2     cli_1.1.0         
[37] magrittr_1.5       crayon_1.3.4       readxl_1.3.1      
[40] evaluate_0.14      fs_1.3.1           fansi_0.4.0       
[43] nlme_3.1-140       rstatix_0.5.0      xml2_1.3.2        
[46] foreign_0.8-71     tools_3.6.1        data.table_1.12.8 
[49] hms_0.5.3          lifecycle_0.1.0    munsell_0.5.0     
[52] reprex_0.3.0       zip_2.0.3          compiler_3.6.1    
[55] rlang_0.4.6        grid_3.6.1         rstudioapi_0.10   
[58] labeling_0.3       rmarkdown_1.13     gtable_0.3.0      
[61] abind_1.4-5        DBI_1.1.0          curl_3.3          
[64] R6_2.4.0           gridExtra_2.3      lubridate_1.7.4   
[67] knitr_1.23         utf8_1.1.4         workflowr_1.6.2   
[70] rprojroot_1.3-2    stringi_1.4.3      Rcpp_1.0.3        
[73] vctrs_0.3.0        dbplyr_1.4.2       tidyselect_1.1.0  
[76] xfun_0.8