Results Output for Question 1
Last updated: 2021-01-14
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Knit directory: esoph-micro-cancer-workflow/
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Question 1
Q1: is there a taxonomic signature shared between the barrett's samples?- Heatmap of relative abundance supervised by sample type: Barrett’s (BO), tumor-adjacent EAC-w/history of barrett’s, EAC-w/ history of barrett’s
- Stacked bar chart of phylum and genus abundance by sample type, same as above
- Additional comparison in TCGA; EAC w/history of Barrett’s vs EAC w/ no history of Barrett’s; same analyses as above
Summary of observations
NCI 16s data
# in long format
table(dat.16s$sample_type)
0 Barretts Only
19800 1320
EAC-adjacent tissue w/ Barretts History EAC tissues w/ Barretts History
11352 9240 dat <- dat.16s %>% filter(OTU == "Fusobacterium_nucleatum")
table(dat$sample_type)
0 Barretts Only
75 5
EAC-adjacent tissue w/ Barretts History EAC tissues w/ Barretts History
43 35 table(dat$Barretts.)
N Y
71 87 5 Barretts samples that were non-EAC tissue related.
TCGA RNAseq data
# in long format
table(dat.rna$sample_type)
0 EAC-adjacent tissue w/ Barretts History
112176 2337
EAC tissues w/ Barretts History
20254 dat <- dat.rna %>% filter(otu2 == "Fusobacterium nucleatum")
table(dat$sample_type)
0 EAC-adjacent tissue w/ Barretts History
144 3
EAC tissues w/ Barretts History
26 table(dat$Barrett.s.Esophagus.Reported)
No Not Available Yes
113 31 29 TCGA WGS data
# in long format
table(dat.wgs$sample_type)
0 EAC-adjacent tissue w/ Barretts History
100491 4674
EAC tissues w/ Barretts History
3116 dat <- dat.wgs %>% filter(otu2 == "Fusobacterium nucleatum")
table(dat$sample_type)
0 EAC-adjacent tissue w/ Barretts History
129 6
EAC tissues w/ Barretts History
4 table(dat$Barrett.s.Esophagus.Reported)
No Not Available Yes
54 47 10 Heatmaps
All OTUs (RA > 0.001)
plot.dat <- dat.16s %>% filter(sample_type != "0", Abundance > 0.001) %>%
mutate(ID = as.factor(accession.number),
Genus = substr(Genus, 4, 1000),
Phylum = substr(Phylum, 4, 1000)) %>%
select(sample_type, Phylum, Genus, ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = ID, y = Genus, fill = Abundance)) +
geom_tile()+
labs(title="NCI 16s Data", subtitle = "Genus Level Data",
x = "ID/Accession Number") +
facet_grid(.~sample_type, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
#ggsave("data/heatmap_nci16s_genus.pdf", p1, units="in", height=23, width=16)plot.dat <- dat.16s %>% filter(sample_type != "0") %>%
mutate(ID = as.factor(accession.number),
Genus = substr(Genus, 4, 1000),
Phylum = substr(Phylum, 4, 1000)) %>%
select(sample_type, Phylum, Genus, ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = ID, y = Phylum, fill = Abundance)) +
geom_tile()+
labs(title="NCI 16s Data", subtitle = "Phylum Level Data",
x = "ID/Accession Number") +
facet_grid(.~sample_type, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
#ggsave("data/heatmap_nci16s_phylum.pdf", p1, units="in", height=10, width=16)plot.dat <- dat.rna %>% filter(sample_type != "0", Abundance > 0.001) %>%
select(sample_type, Phylum, Genus, Patient_ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = Patient_ID, y = Genus, fill = Abundance)) +
geom_tile()+
labs(title="TCGA RNAseq Data", subtitle = "Genus Level Data",
x = "ID/Accession Number") +
facet_grid(.~sample_type, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
#ggsave("data/heatmap_tcgarna_genus.pdf", p1, units="in", height=23, width=16)plot.dat <- dat.rna %>% filter(sample_type != "0") %>%
select(sample_type, Phylum, Genus, Patient_ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = Patient_ID, y = Phylum, fill = Abundance)) +
geom_tile()+
labs(title="NCI 16s Data", subtitle = "Phylum Level Data",
x = "ID/Accession Number") +
facet_grid(.~sample_type, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
plot.dat <- dat.wgs %>% filter(sample_type != "0", Abundance > 0.001) %>%
select(sample_type, Phylum, Genus, Patient_ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = Patient_ID, y = Genus, fill = Abundance)) +
geom_tile()+
labs(title="NCI 16s Data", subtitle = "Genus Level Data",
x = "ID/Accession Number") +
facet_grid(.~sample_type, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
#ggsave("data/heatmap_nci16s_genus.pdf", p1, units="in", height=23, width=16)plot.dat <- dat.wgs %>% filter(sample_type != "0") %>%
select(sample_type, Phylum, Genus, Patient_ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = Patient_ID, y = Phylum, fill = Abundance)) +
geom_tile()+
labs(title="NCI 16s Data", subtitle = "Phylum Level Data",
x = "ID/Accession Number") +
facet_grid(.~sample_type, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
Specific OTUs
plot.dat <- dat.16s.s %>% filter(sample_type != "0") %>%
mutate(ID = as.factor(accession.number),
Genus = substr(Genus, 4, 1000),
Phylum = substr(Phylum, 4, 1000)) %>%
select(sample_type, Phylum, Genus, OTU, ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = ID, y = OTU, fill = Abundance)) +
geom_tile()+
labs(title="NCI 16s Data", y=NULL,
x = "ID/Accession Number") +
facet_grid(.~sample_type, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
plot.dat <- dat.rna.s %>% filter(sample_type != "0", is.na(OTU1) == F) %>%
select(sample_type, Phylum, Genus, OTU, Patient_ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = Patient_ID, y = OTU, fill = Abundance)) +
geom_tile()+
labs(title="TCGA RNAseq Data", y=NULL,
x = "ID/Accession Number") +
facet_grid(.~sample_type, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
plot.dat <- dat.wgs.s %>% filter(sample_type != "0", is.na(OTU1) == F) %>%
select(sample_type, Phylum, Genus, OTU, Patient_ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = Patient_ID, y = OTU, fill = Abundance)) +
geom_tile()+
labs(title="TCGA WGS Data", y=NULL,
x = "ID/Accession Number") +
facet_grid(.~sample_type, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
Stacked Bar Charts
All OTUs (RA > 0.001)
plot.dat <- dat.16s %>% filter(sample_type != "0", Abundance > 0.01 ) %>%
mutate(ID = as.factor(accession.number),
Genus = substr(Genus, 4, 1000),
Phylum = substr(Phylum, 4, 1000))%>%
dplyr::group_by(sample_type, Genus)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=sample_type, y = Abundance, fill=Genus)) +
geom_bar(stat="identity")+
labs(title="NCI 16s Data",
subtitle = "Genus Level Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()+
theme(legend.position = "none")
p1
TOO MANY LEVELS FOR IT TO MAKE SENSE
plot.dat <- dat.16s %>% filter(sample_type != "0") %>%
mutate(ID = as.factor(accession.number),
Genus = substr(Genus, 4, 1000),
Phylum = substr(Phylum, 4, 1000))%>%
dplyr::group_by(sample_type, Phylum)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=sample_type, y = Abundance, fill=Phylum)) +
geom_bar(stat="identity")+
labs(title="NCI 16s Data",
subtitle = "Phylum Level Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1 
plot.dat <- dat.rna %>% filter(sample_type != "0", Abundance > 0.001)%>%
dplyr::group_by(sample_type, Genus)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=sample_type, y = Abundance, fill=Genus)) +
geom_bar(stat="identity")+
labs(title="TCGA RNAseq Data",
subtitle = "Genus Level Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
#ggsave("data/bar_tcgarna_genus.pdf", p1, units="in", height=23, width=16)plot.dat <- dat.rna %>% filter(sample_type != "0")%>%
dplyr::group_by(sample_type, Phylum)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=sample_type, y = Abundance, fill=Phylum)) +
geom_bar(stat="identity")+
labs(title="TCGA RNAseq Data",
subtitle = "Phylum Level Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
plot.dat <- dat.wgs %>% filter(sample_type != "0", Abundance > 0.001)%>%
dplyr::group_by(sample_type, Genus)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=sample_type, y = Abundance, fill=Genus)) +
geom_bar(stat="identity")+
labs(title="TCGA WGS Data",
subtitle = "Genus Level Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
plot.dat <- dat.wgs %>% filter(sample_type != "0")%>%
dplyr::group_by(sample_type, Phylum)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=sample_type, y = Abundance, fill=Phylum)) +
geom_bar(stat="identity")+
labs(title="TCGA WGS Data",
subtitle = "Phylum Level Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
Specific OTUs
plot.dat <- dat.16s.s %>% filter(sample_type != "0") %>%
mutate(ID = as.factor(accession.number),
Genus = substr(Genus, 4, 1000),
Phylum = substr(Phylum, 4, 1000))%>%
dplyr::group_by(sample_type, OTU1)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=sample_type, y = Abundance, fill=OTU1)) +
geom_bar(stat="identity")+
labs(title="NCI 16s Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
plot.dat <- dat.rna.s %>% filter(sample_type != "0", is.na(OTU1) == F)%>%
dplyr::group_by(sample_type, OTU1)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=sample_type, y = Abundance, fill=OTU1)) +
geom_bar(stat="identity")+
labs(title="NCI 16s Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
plot.dat <- dat.wgs.s %>% filter(sample_type != "0", is.na(OTU1) == F)%>%
dplyr::group_by(sample_type, OTU1)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'sample_type' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=sample_type, y = Abundance, fill=OTU1)) +
geom_bar(stat="identity")+
labs(title="TCGA WGS Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
EAC Barretts to No Barretts Comparison
Heatmaps
All OTUs (RA > 0.001)
plot.dat <- dat.rna %>% filter(EACcomp != "0", Abundance > 0.001)
p1 <- ggplot(plot.dat, aes(x = Patient_ID, y = Genus, fill = Abundance)) +
geom_tile()+
labs(title="TCGA RNAseq Data", subtitle = "Genus Level Data",
x = "ID/Accession Number") +
facet_grid(.~EACcomp, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
#ggsave("data/heatmap_tcgarna_genus.pdf", p1, units="in", height=23, width=16)plot.dat <- dat.rna %>% filter(EACcomp != "0") %>%
select(EACcomp, Phylum, Genus, Patient_ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = Patient_ID, y = Phylum, fill = Abundance)) +
geom_tile()+
labs(title="TCGA RNAseq Data", subtitle = "Phylum Level Data",
x = "ID/Accession Number") +
facet_grid(.~EACcomp, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.001)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
plot.dat <- dat.wgs %>% filter(EACcomp != "0", Abundance > 0.001) %>%
select(EACcomp, Phylum, Genus, Patient_ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = Patient_ID, y = Genus, fill = Abundance)) +
geom_tile()+
labs(title="TCGA WGS Data", subtitle = "Genus Level Data",
x = "ID/Accession Number") +
facet_grid(.~EACcomp, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
plot.dat <- dat.wgs %>% filter(EACcomp != "0") %>%
select(EACcomp, Phylum, Genus, Patient_ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = Patient_ID, y = Phylum, fill = Abundance)) +
geom_tile()+
labs(title="TCGA WGS Data", subtitle = "Phylum Level Data",
x = "ID/Accession Number") +
facet_grid(.~EACcomp, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.001)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
Specific OTUs
plot.dat <- dat.rna.s %>% filter(EACcomp != "0", is.na(OTU1) == F) %>%
select(EACcomp, OTU1, Patient_ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x = Patient_ID, y = OTU1, fill = Abundance)) +
geom_tile()+
labs(title="TCGA RNAseq Data", y=NULL,
x = "ID/Accession Number") +
facet_grid(.~EACcomp, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.1)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
plot.dat <- dat.wgs.s %>% filter(EACcomp != "0", is.na(OTU1) == F) %>%
select(EACcomp, OTU1, Patient_ID, Abundance)
plot.dat <- na.omit(plot.dat)
p1 <- ggplot(plot.dat, aes(x =Patient_ID, y = OTU1, fill = Abundance)) +
geom_tile()+
labs(title="TCGA WGS Data", y=NULL,
x = "ID/Accession Number") +
facet_grid(.~EACcomp, scales="free")+
scale_fill_gradient(low="white", high="black", trans="sqrt", limits=c(0, 0.5)) +
theme_classic()+
theme(
axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5),
strip.text.y = element_text(angle = 0)
)
p1
Stacked Bar Charts
All OTUs (RA > 0.001)
plot.dat <- dat.rna %>% filter(EACcomp != "0", Abundance > 0.001)%>%
dplyr::group_by(EACcomp, Genus)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'EACcomp' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=EACcomp, y = Abundance, fill=Genus)) +
geom_bar(stat="identity")+
labs(title="TCGA RNAseq Data",
subtitle = "Genus Level Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
#ggsave("data/bar_tcgarna_genus.pdf", p1, units="in", height=23, width=16)plot.dat <- dat.rna %>% filter(EACcomp != "0")%>%
dplyr::group_by(EACcomp, Phylum)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'EACcomp' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=EACcomp, y = Abundance, fill=Phylum)) +
geom_bar(stat="identity")+
labs(title="TCGA RNAseq Data",
subtitle = "Phylum Level Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
plot.dat <- dat.wgs %>% filter(EACcomp != "0", Abundance > 0.001)%>%
dplyr::group_by(EACcomp, Genus)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'EACcomp' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=EACcomp, y = Abundance, fill=Genus)) +
geom_bar(stat="identity")+
labs(title="TCGA WGS Data",
subtitle = "Genus Level Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
plot.dat <- dat.wgs %>% filter(EACcomp != "0")%>%
dplyr::group_by(EACcomp, Phylum)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'EACcomp' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=EACcomp, y = Abundance, fill=Phylum)) +
geom_bar(stat="identity")+
labs(title="TCGA WGS Data",
subtitle = "Phylum Level Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
Specific OTUs
plot.dat <- dat.rna.s %>% filter(EACcomp != "0", is.na(OTU1) == F)%>%
dplyr::group_by(EACcomp, OTU1)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'EACcomp' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=EACcomp, y = Abundance, fill=OTU1)) +
geom_bar(stat="identity")+
labs(title="TCGA RNA seq Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
plot.dat <- dat.wgs.s %>% filter(EACcomp != "0", is.na(OTU1) == F)%>%
dplyr::group_by(EACcomp, OTU1)%>%
dplyr::summarise(
Abundance = mean(Abundance, na.rm=T)
)`summarise()` regrouping output by 'EACcomp' (override with `.groups` argument)p1 <- ggplot(plot.dat, aes(x=EACcomp, y = Abundance, fill=OTU1)) +
geom_bar(stat="identity")+
labs(title="TCGA WGS Data",
x = "Tissue Group",
y="Average Relative Abundance") +
theme_classic()
p1
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] car_3.0-8 carData_3.0-4 gvlma_1.0.0.3 patchwork_1.0.1
[5] viridis_0.5.1 viridisLite_0.3.0 gridExtra_2.3 xtable_1.8-4
[9] kableExtra_1.1.0 plyr_1.8.6 data.table_1.13.0 readxl_1.3.1
[13] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.1 purrr_0.3.4
[17] readr_1.3.1 tidyr_1.1.1 tibble_3.0.3 ggplot2_3.3.2
[21] tidyverse_1.3.0 lmerTest_3.1-2 lme4_1.1-23 Matrix_1.2-18
[25] vegan_2.5-6 lattice_0.20-41 permute_0.9-5 phyloseq_1.32.0
[29] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] minqa_1.2.4 colorspace_1.4-1 rio_0.5.16
[4] ellipsis_0.3.1 rprojroot_1.3-2 XVector_0.28.0
[7] fs_1.5.0 rstudioapi_0.11 farver_2.0.3
[10] fansi_0.4.1 lubridate_1.7.9 xml2_1.3.2
[13] codetools_0.2-16 splines_4.0.2 knitr_1.29
[16] ade4_1.7-15 jsonlite_1.7.0 nloptr_1.2.2.2
[19] broom_0.7.0 cluster_2.1.0 dbplyr_1.4.4
[22] BiocManager_1.30.10 compiler_4.0.2 httr_1.4.2
[25] backports_1.1.7 assertthat_0.2.1 cli_2.0.2
[28] later_1.1.0.1 htmltools_0.5.0 tools_4.0.2
[31] igraph_1.2.5 gtable_0.3.0 glue_1.4.1
[34] reshape2_1.4.4 Rcpp_1.0.5 Biobase_2.48.0
[37] cellranger_1.1.0 vctrs_0.3.2 Biostrings_2.56.0
[40] multtest_2.44.0 ape_5.4 nlme_3.1-148
[43] iterators_1.0.12 xfun_0.19 openxlsx_4.1.5
[46] rvest_0.3.6 lifecycle_0.2.0 statmod_1.4.34
[49] zlibbioc_1.34.0 MASS_7.3-51.6 scales_1.1.1
[52] hms_0.5.3 promises_1.1.1 parallel_4.0.2
[55] biomformat_1.16.0 rhdf5_2.32.2 curl_4.3
[58] yaml_2.2.1 stringi_1.4.6 S4Vectors_0.26.1
[61] foreach_1.5.0 BiocGenerics_0.34.0 zip_2.0.4
[64] boot_1.3-25 rlang_0.4.7 pkgconfig_2.0.3
[67] evaluate_0.14 Rhdf5lib_1.10.1 labeling_0.3
[70] tidyselect_1.1.0 magrittr_1.5 R6_2.4.1
[73] IRanges_2.22.2 generics_0.0.2 DBI_1.1.0
[76] foreign_0.8-80 pillar_1.4.6 haven_2.3.1
[79] whisker_0.4 withr_2.2.0 mgcv_1.8-31
[82] abind_1.4-5 survival_3.2-3 modelr_0.1.8
[85] crayon_1.3.4 rmarkdown_2.5 grid_4.0.2
[88] blob_1.2.1 git2r_0.27.1 reprex_0.3.0
[91] digest_0.6.25 webshot_0.5.2 httpuv_1.5.4
[94] numDeriv_2016.8-1.1 stats4_4.0.2 munsell_0.5.0