- Data Setup
- Import DGElist Data
- GO Analysis
- Visualisation
- Visualisation
- Visualisation
- Export Data
GO Analysis
Ha Tran
22/08/2021
Last updated: 2022-11-05
Checks: 7 0
Knit directory: SRB_2022/1_analysis/
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Data Setup
# working with data
library(dplyr)
library(magrittr)
library(readr)
library(tibble)
library(reshape2)
library(tidyverse)
# Visualisation:
library(kableExtra)
library(ggplot2)
library(grid)
# Custom ggplot
library(gridExtra)
library(ggbiplot)
library(ggrepel)
# Bioconductor packages:
library(edgeR)
library(limma)
library(Glimma)
library(clusterProfiler)
library(org.Mm.eg.db)
library(enrichplot)
theme_set(theme_minimal())
pub <- readRDS(here::here("0_data/RDS_objects/pub.rds"))Import DGElist Data
DGElist object containing the raw feature count, sample metadata, and gene metadata, created in the Set Up stage.
# load DGElist previously created in the set up
dge <- readRDS(here::here("0_data/RDS_objects/dge.rds"))
fc <- readRDS(here::here("0_data/RDS_objects/fc.rds"))
lfc <- readRDS(here::here("0_data/RDS_objects/lfc.rds"))
lmTreat <- readRDS(here::here("0_data/RDS_objects/lmTreat.rds"))
lmTreat_sig <- readRDS(here::here("0_data/RDS_objects/lmTreat_sig.rds"))GO Analysis
goSummaries is a package created by Dr Stephen Pederson
for filtering GO terms based on ontology level.
# download go summaries and set the minimum ontology level
goSummaries <- url("https://uofabioinformaticshub.github.io/summaries2GO/data/goSummaries.RDS") %>%
readRDS()
minPath <- 3
enrichGO=list()
enrichGO_sig <- list()
for (i in 1:length(fc)) {
x <- fc[i] %>% as.character()
# find enriched GO terms
enrichGO[[x]] <- clusterProfiler::enrichGO(
gene = lmTreat_sig[[x]]$entrezid,
OrgDb = org.Mm.eg.db,
keyType = "ENTREZID",
ont = "ALL",
pAdjustMethod = "fdr",
pvalueCutoff = 0.05
)
# bind to goSummaries to elminate go terms with ontology levels 1 and 2.
enrichGO_sig[[x]] <- enrichGO[[x]] %>%
as.data.frame() %>%
rownames_to_column("id") %>%
left_join(goSummaries) %>%
dplyr::filter(shortest_path >= minPath) %>%
column_to_rownames("id")
# adjust go results, separate compound column, add FDR column, adjust the GeneRatio column
enrichGO_sig[[x]] <- enrichGO_sig[[x]] %>%
separate(col = BgRatio, sep = "/", into = c("Total", "Universe")) %>%
dplyr::mutate(
logFDR = -log(p.adjust, 10),
GeneRatio = Count / as.numeric(Total)) %>%
dplyr::select(c("Count", "GeneRatio", "ontology", "pvalue", "p.adjust", "logFDR", "qvalue", "Description", "geneID"))
# at the beginnning of a word (after 35 characters), add a newline. shorten the y axis for dot plot
enrichGO_sig[[x]]$Description <- sub(pattern = "(.{1,35})(?:$| )",
replacement = "\\1\n",
x = enrichGO_sig[[x]]$Description)
# remove the additional newline at the end of the string
enrichGO_sig[[x]]$Description <- sub(pattern = "\n$",
replacement = "",
x = enrichGO_sig[[x]]$Description)
}# display the top 30 most sig
enrichGO_sig[[1]][1:30, ] %>%
kable(caption = "Top 30 significantly enriched GO terms") %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Count | GeneRatio | ontology | pvalue | p.adjust | logFDR | qvalue | Description | geneID | |
|---|---|---|---|---|---|---|---|---|---|
| GO:0030198 | 66 | 0.2095238 | BP | 0 | 0 | 20.27079 | 0 | extracellular matrix organization | 12814/16147/13078/17389/545370/20319/74199/20356/219151/12818/18214/223838/94216/70779/208177/114249/94214/23871/107581/21810/271127/240322/14268/17390/15227/14230/18073/320078/15117/268780/11504/12840/12817/50706/16950/224697/64075/100952/18383/21846/12832/68169/108153/16998/58223/12819/77739/56401/246228/320712/56429/14219/58859/56693/241327/12389/80883/237759/12822/241226/233332/17022/67896/23876/12830/13805 |
| GO:0043062 | 66 | 0.2088608 | BP | 0 | 0 | 20.27079 | 0 | extracellular structure organization | 12814/16147/13078/17389/545370/20319/74199/20356/219151/12818/18214/223838/94216/70779/208177/114249/94214/23871/107581/21810/271127/240322/14268/17390/15227/14230/18073/320078/15117/268780/11504/12840/12817/50706/16950/224697/64075/100952/18383/21846/12832/68169/108153/16998/58223/12819/77739/56401/246228/320712/56429/14219/58859/56693/241327/12389/80883/237759/12822/241226/233332/17022/67896/23876/12830/13805 |
| GO:0045229 | 66 | 0.2082019 | BP | 0 | 0 | 20.27079 | 0 | external encapsulating structure organization | 12814/16147/13078/17389/545370/20319/74199/20356/219151/12818/18214/223838/94216/70779/208177/114249/94214/23871/107581/21810/271127/240322/14268/17390/15227/14230/18073/320078/15117/268780/11504/12840/12817/50706/16950/224697/64075/100952/18383/21846/12832/68169/108153/16998/58223/12819/77739/56401/246228/320712/56429/14219/58859/56693/241327/12389/80883/237759/12822/241226/233332/17022/67896/23876/12830/13805 |
| GO:0045785 | 79 | 0.1639004 | BP | 0 | 0 | 17.94285 | 0 | positive regulation of cell adhesion | 16147/13643/74199/140709/11600/17242/16842/16401/12522/16542/16000/114249/18186/54371/12505/218952/94214/23871/107581/14268/15227/15894/18073/21687/12554/20315/15117/268780/104709/14634/27205/12310/21838/67916/24099/12721/12479/68606/64075/16408/14961/50931/100952/22341/20667/171285/15002/20339/16002/68169/26903/105855/16963/18552/14969/20851/56349/320712/11492/14960/317757/58859/20443/22637/83408/54519/19242/16161/12389/18806/16186/30963/20737/18606/12162/16197/12504/320484/67896 |
| GO:0006816 | 73 | 0.1659091 | BP | 0 | 0 | 16.78590 | 0 | calcium ion transport | 338370/12288/20190/319984/20730/16000/11549/20541/18127/13491/320508/12293/13618/17918/238384/15894/14812/18760/20855/12766/20315/94249/12290/109676/110893/12310/22068/21838/270028/12721/14612/23796/381812/11607/13617/26903/30948/11517/15558/16963/18763/66109/81904/217154/74777/216869/65973/18764/14360/23832/20192/12523/56437/54598/58226/66972/19218/381290/14219/14697/317757/68312/98660/83408/19164/109552/18596/12389/12286/53376/12298/14062/12504 |
| GO:0050808 | 77 | 0.1558704 | BP | 0 | 0 | 16.25596 | 0 | synapse organization | 23888/14432/237979/241568/235611/19266/20450/192167/18186/19277/242662/55983/231602/12558/245880/66725/272381/17918/17260/18645/18164/14812/210274/93706/98733/330814/327814/110893/386750/67784/210293/14658/329165/16560/68507/72333/13837/245537/217480/73340/11816/442801/269116/50791/260297/13602/232560/219228/73181/13841/70237/238988/70530/14360/13385/13048/18483/71228/240057/53972/236915/67790/19164/19242/80883/12286/93707/59036/243621/228880/12298/14062/228357/52163/216856/216049/12830 |
| GO:0034329 | 71 | 0.1609977 | BP | 0 | 0 | 15.65561 | 0 | cell junction assembly | 23888/14432/237979/22411/16542/235611/19266/20450/192167/13823/208177/17475/18186/19277/218952/107581/12558/14268/272381/12563/17260/18164/83964/56229/21687/210274/98733/330814/54420/320873/386750/270163/67784/12562/21838/329165/68606/13837/23796/69524/245537/20401/77569/11856/73340/269116/12552/50791/14615/18613/20613/219228/13841/77446/50768/233651/70237/53885/12741/13048/71228/236915/15257/12389/12286/192897/18571/18606/12737/228357/216856 |
| GO:0031589 | 62 | 0.1662198 | BP | 0 | 0 | 14.12428 | 0 | cell-substrate adhesion | 19283/74199/140709/11600/17242/16401/16542/208177/114249/18186/23928/218952/94214/107581/16421/14268/15227/18073/83964/56229/21687/12554/15117/268780/109700/12817/329872/21838/50706/12721/68606/64075/13837/16408/77569/11856/100952/22341/208777/15434/18613/56363/68169/16404/64099/18552/170736/50768/105298/56349/320712/14219/58859/19242/84544/80883/241226/192897/30963/18606/18074/67896 |
| GO:0048754 | 43 | 0.2239583 | BP | 0 | 0 | 13.99703 | 0 | branching morphogenesis of an epithelial tube | 16147/20319/20356/22420/11835/11600/15245/17242/16842/15431/16542/18121/16000/21385/114249/18186/12505/15396/271127/14734/11839/15227/21687/20315/21412/14634/67784/238057/17313/11607/21386/69903/21846/13617/18763/73181/19206/233651/71228/329628/12162/17869/13805 |
| GO:0007224 | 39 | 0.2452830 | BP | 0 | 0 | 13.98732 | 0 | smoothened signaling pathway | 14632/16147/15245/68525/18121/19207/59056/16576/56297/72507/14734/15227/68099/20720/71492/78795/94187/14634/218232/73916/216795/19376/240888/18605/110350/15258/67884/264134/56350/19206/234740/140810/19335/66573/71228/83396/15257/71951/12589 |
| GO:0001655 | 62 | 0.1602067 | BP | 0 | 0 | 13.50225 | 0 | urogenital system development | 20897/22420/11835/11600/22411/72135/15431/13123/18121/16000/114249/18186/19277/12505/15396/271127/14734/66725/13618/17390/17260/15227/15903/15904/107587/18073/13809/21687/14561/11504/21412/14634/67784/14725/243931/12142/73692/18605/12577/11607/110350/13617/56198/18763/18552/56350/55994/13841/19206/233651/23967/18764/66333/71228/329628/18596/83396/241226/12162/228357/13003/17869 |
| GO:0001822 | 56 | 0.1696970 | BP | 0 | 0 | 13.16257 | 0 | kidney development | 20897/22420/11600/22411/72135/15431/18121/114249/18186/19277/12505/15396/271127/14734/66725/13618/17260/15903/107587/18073/13809/21687/14561/11504/21412/14634/67784/14725/243931/12142/73692/18605/12577/11607/110350/13617/56198/18763/18552/56350/55994/13841/19206/233651/23967/18764/66333/71228/329628/18596/83396/241226/12162/228357/13003/17869 |
| GO:0072001 | 57 | 0.1652174 | BP | 0 | 0 | 12.95421 | 0 | renal system development | 20897/22420/11600/22411/72135/15431/18121/114249/18186/19277/12505/15396/271127/14734/66725/13618/17260/15227/15903/107587/18073/13809/21687/14561/11504/21412/14634/67784/14725/243931/12142/73692/18605/12577/11607/110350/13617/56198/18763/18552/56350/55994/13841/19206/233651/23967/18764/66333/71228/329628/18596/83396/241226/12162/228357/13003/17869 |
| GO:0034765 | 70 | 0.1405622 | BP | 0 | 0 | 12.58819 | 0 | regulation of ion transmembrane transport | 98741/338370/16519/12288/329152/16494/16508/56543/192167/77574/20541/399548/13491/18301/20265/12293/226922/17918/17260/18760/12766/12290/109676/13616/18795/22068/21838/12721/110876/23796/245537/381812/11607/260297/16531/13617/99738/26903/30948/66109/81904/217154/56461/74777/65973/23967/18764/14199/14360/56437/58226/13385/66733/19218/381290/20269/14697/68312/98660/19164/18671/109552/12389/60613/12286/12298/14062/16510/22160/216856 |
| GO:0001667 | 66 | 0.1460177 | BP | 0 | 0 | 12.58819 | 0 | ameboidal-type cell migration | 13078/20356/11600/22411/16401/16542/16000/14026/24136/18214/20357/20541/18127/18186/20361/23871/12558/16421/14268/13618/17260/18645/19245/18760/20855/21687/12554/20315/15117/83397/238328/13616/19274/12310/67784/12562/71709/67916/68606/16590/240185/20401/22341/72446/11816/13617/218877/76441/18613/16002/17311/79221/23797/381290/14314/11881/78560/20358/212307/114886/192897/18606/12162/15111/22160/269608 |
| GO:0048736 | 42 | 0.2058824 | BP | 0 | 0 | 12.55761 | 0 | appendage development | 16147/20319/12288/16842/15430/15431/18121/16764/106522/21385/225743/218952/15396/14734/15438/15395/68099/107587/71492/226844/14634/216795/64075/73692/18605/21386/110350/18552/15405/19206/234740/65973/23967/140810/19335/19164/192897/74239/12162/228357/15111/22160 |
| GO:0060173 | 42 | 0.2058824 | BP | 0 | 0 | 12.55761 | 0 | limb development | 16147/20319/12288/16842/15430/15431/18121/16764/106522/21385/225743/218952/15396/14734/15438/15395/68099/107587/71492/226844/14634/216795/64075/73692/18605/21386/110350/18552/15405/19206/234740/65973/23967/140810/19335/19164/192897/74239/12162/228357/15111/22160 |
| GO:0031345 | 43 | 0.2000000 | BP | 0 | 0 | 12.44247 | 0 | negative regulation of cell projection organization | 13643/19283/17756/20356/14026/20357/192167/18186/20361/121021/66725/235106/66610/13131/18645/14812/22068/21838/13837/209743/245537/244152/12494/11816/218877/19347/73181/237847/13841/18007/14360/270120/233781/22240/240057/74201/53972/19164/20358/29869/228357/70433/216049 |
| GO:0060562 | 60 | 0.1518987 | BP | 0 | 0 | 12.15183 | 0 | epithelial tube morphogenesis | 16147/20319/20356/22420/11835/11600/15245/17242/16842/15431/16542/18121/16000/24136/21385/114249/18186/12505/15396/271127/14734/11839/17260/15227/21687/20315/21412/14634/73916/67784/238057/14725/330409/17313/23796/11607/21386/69903/21846/13617/106042/18763/73181/13841/69718/50768/19206/233651/23967/18764/19335/57265/71228/329628/19164/12162/15111/17869/22160/13805 |
| GO:0035107 | 38 | 0.2183908 | BP | 0 | 0 | 12.15183 | 0 | appendage morphogenesis | 16147/20319/12288/16842/15430/15431/18121/16764/106522/21385/225743/15396/14734/15438/15395/68099/107587/226844/14634/216795/73692/18605/21386/110350/18552/15405/19206/234740/65973/23967/140810/19335/19164/74239/12162/228357/15111/22160 |
| GO:0035108 | 38 | 0.2183908 | BP | 0 | 0 | 12.15183 | 0 | limb morphogenesis | 16147/20319/12288/16842/15430/15431/18121/16764/106522/21385/225743/15396/14734/15438/15395/68099/107587/226844/14634/216795/73692/18605/21386/110350/18552/15405/19206/234740/65973/23967/140810/19335/19164/74239/12162/228357/15111/22160 |
| GO:0006874 | 69 | 0.1380000 | BP | 0 | 0 | 12.13111 | 0 | cellular calcium ion homeostasis | 16527/12288/16542/20190/11549/20541/231602/19309/51800/12293/13618/17918/238384/234515/78134/14812/18760/20855/12766/94249/12290/19220/109676/13616/110893/12310/22068/12562/21838/19228/270028/12721/14806/23796/72844/12494/11607/11816/13617/12062/11517/15558/16963/18763/74777/65973/18764/14360/23832/20192/66972/13385/57265/19218/381290/317757/68312/98660/83408/19164/109552/12389/12286/12298/14062/12504/16510/23833/19217 |
| GO:0061138 | 44 | 0.1913043 | BP | 0 | 0 | 12.12965 | 0 | morphogenesis of a branching epithelium | 16147/15234/20319/20356/22420/11835/11600/15245/17242/16842/15431/16542/18121/16000/21385/114249/18186/12505/15396/271127/14734/11839/15227/21687/20315/21412/14634/67784/238057/17313/11607/21386/69903/21846/13617/18763/73181/19206/233651/71228/329628/12162/17869/13805 |
| GO:0007409 | 68 | 0.1379310 | BP | 0 | 0 | 11.95313 | 0 | axonogenesis | 14432/13842/235472/13643/19283/17756/20356/16401/241568/26565/13176/235611/18121/14026/24136/20357/225743/18186/19277/20361/12558/14268/13131/17260/18164/52666/20315/13616/14634/386750/19274/67784/238057/14725/21838/17984/16773/13837/17181/245537/244152/11816/269116/12552/13617/218877/18080/237847/13841/18007/246048/19206/22253/240057/381979/19164/20358/29869/68404/80883/12286/12162/228357/58208/16572/20564/70433/18223 |
| GO:0051924 | 49 | 0.1707317 | BP | 0 | 0 | 11.69273 | 0 | regulation of calcium ion transport | 12288/319984/20730/16000/20541/18127/13491/12293/17918/15894/18760/20855/12766/20315/109676/12310/22068/21838/12721/23796/381812/11607/13617/26903/30948/11517/66109/217154/74777/216869/65973/18764/14360/12523/56437/19218/14697/317757/68312/98660/83408/109552/18596/12389/12286/53376/12298/14062/12504 |
| GO:0098742 | 41 | 0.1915888 | BP | 0 | 0 | 11.26136 | 0 | cell-cell adhesion via plasma-membrane adhesion molecules | 23888/235472/73173/545370/237979/84004/16401/241568/19266/192167/12558/272381/12563/23965/13131/12554/93706/98733/330814/320873/386750/19274/12562/279653/53601/72333/13837/16408/69524/12552/50791/13602/20339/18613/219228/233651/270120/329628/93885/80883/12737 |
| GO:0050673 | 65 | 0.1365546 | BP | 0 | 0 | 11.18814 | 0 | epithelial cell proliferation | 14632/16147/15234/20319/20356/11835/17242/16401/235505/16542/216439/13123/18121/16000/21385/68888/14313/12444/14734/13618/11839/17260/107587/18760/12766/21687/12554/20315/15117/238328/20913/19274/12310/73916/16590/228852/23796/240185/12577/22341/11607/11816/21846/13617/16002/26903/16601/13345/19206/23967/66333/23797/30878/353156/19164/19242/12389/16010/226841/12737/67866/58208/17869/22160/13805 |
| GO:0060402 | 37 | 0.2067039 | BP | 0 | 0 | 11.11159 | 0 | calcium ion transport into cytosol | 12288/20190/11549/20541/12293/17918/238384/14812/18760/12766/12290/109676/110893/12310/21838/270028/12721/23796/11607/13617/11517/15558/16963/74777/65973/18764/14360/23832/20192/317757/68312/83408/109552/12389/12286/14062/12504 |
| GO:0031346 | 62 | 0.1399549 | BP | 0 | 0 | 11.11159 | 0 | positive regulation of cell projection organization | 19283/15234/20356/216739/235180/17242/13176/235611/19266/24136/192167/108686/242274/18186/20361/14268/23965/18760/20720/20315/224617/98733/11504/64297/67784/20713/329165/16590/13837/72844/19888/67425/11816/50791/230872/232560/68169/18080/56401/246048/70237/140810/14360/66573/13385/13048/18483/22240/58804/11881/23854/19242/71951/12877/234776/228880/18606/26563/12162/269254/52163/18223 |
| GO:0010977 | 35 | 0.2160494 | BP | 0 | 0 | 11.05385 | 0 | negative regulation of neuron projection development | 13643/19283/17756/20356/20357/192167/18186/20361/121021/66725/235106/13131/21838/13837/209743/245537/244152/12494/11816/218877/19347/237847/13841/18007/270120/233781/22240/240057/53972/19164/20358/29869/228357/70433/216049 |
Visualisation
bp_dot=list()
mf_dot=list()
cc_dot=list()
upset=list()
for (i in 1:length(fc)) {
x <- fc[i] %>% as.character()
# extract the enriched GO terms from each ontology
bp <- enrichGO_sig[[x]] %>% dplyr::filter(ontology == "BP")
mf <- enrichGO_sig[[x]] %>% dplyr::filter(ontology == "MF")
cc <- enrichGO_sig[[x]] %>% dplyr::filter(ontology == "CC")
# bp dot plot, save
bp_dot[[x]] <- ggplot(bp[1:15, ]) +
geom_point(aes(x = GeneRatio, y = reorder(Description, GeneRatio), colour = logFDR, size = Count)) +
scale_color_gradient(low = "dodgerblue3", high = "firebrick3", limits = c(0, NA)) +
scale_size(range = c(.3,3)) +
ggtitle("Biological Process") +
ylab(label = "") +
xlab(label = "Gene Ratio") +
labs(color = expression("-log"[10] * "FDR"), size = "Gene Counts")
ggsave(filename = paste0("bp_dot_", fc[i], ".svg"), plot = bp_dot[[x]], path = here::here("2_plots/go/"),
width = 88, height = 95, units = "mm")
# mf dot plot, save
mf_dot[[x]] <- ggplot(mf[1:15, ]) +
geom_point(aes(x = GeneRatio, y = reorder(Description, GeneRatio), colour = logFDR, size = Count)) +
scale_color_gradient(low = "dodgerblue3", high = "firebrick3", limits = c(0, NA)) +
scale_size(range = c(.3,3)) +
ggtitle("Molecular Function") +
ylab(label = "") +
xlab(label = "Gene Ratio") +
labs(color = expression("-log"[10] * "FDR"), size = "Gene Counts")
ggsave(filename = paste0("mf_dot_", fc[i], ".svg"), plot = mf_dot[[x]], path = here::here("2_plots/go/"),
width = 88, height = 95, units = "mm")
# cc dot plot, save
cc_dot[[x]] <- ggplot(cc[1:15, ]) +
geom_point(aes(x = GeneRatio, y = reorder(Description, GeneRatio), colour = logFDR, size = Count)) +
scale_color_gradient(low = "dodgerblue3", high = "firebrick3", limits = c(0, NA)) +
scale_size(range = c(.3,3)) +
ggtitle("Cellular Components") +
ylab(label = "") +
xlab(label = "Gene Ratio") +
labs(color = expression("-log"[10] * "FDR"), size = "Gene Counts")
ggsave(filename = paste0("cc_dot_", fc[i], ".svg"), plot = cc_dot[[x]], path = here::here("2_plots/go/"),
width = 88, height = 95, units = "mm")
upset[[x]] <- upsetplot(x = enrichGO[[x]], 10)
ggsave(filename = paste0("upset_", fc[i], ".svg"), plot = upset[[x]], path = here::here("2_plots/go/"))
}bp_dot[[1]] 
mf_dot[[1]]
cc_dot[[1]]
upset[[1]]
# display the top 30 most sig
enrichGO_sig[[2]][1:30, ] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Count | GeneRatio | ontology | pvalue | p.adjust | logFDR | qvalue | Description | geneID | |
|---|---|---|---|---|---|---|---|---|---|
| GO:0030198 | 61 | 0.1936508 | BP | 0 | 0 | 19.430998 | 0 | extracellular matrix organization | 12814/16147/13078/17389/545370/20319/74199/20356/219151/12818/223838/94216/18214/70779/114249/208177/94214/271127/21810/23871/240322/14268/17390/15227/107581/14230/18073/320078/15117/268780/11504/12840/12817/50706/64075/16950/224697/18383/100952/21846/68169/108153/12832/12819/16998/58223/77739/56401/246228/320712/56429/14219/56693/58859/241327/237759/80883/233332/12389/12822/241226 |
| GO:0043062 | 61 | 0.1930380 | BP | 0 | 0 | 19.430998 | 0 | extracellular structure organization | 12814/16147/13078/17389/545370/20319/74199/20356/219151/12818/223838/94216/18214/70779/114249/208177/94214/271127/21810/23871/240322/14268/17390/15227/107581/14230/18073/320078/15117/268780/11504/12840/12817/50706/64075/16950/224697/18383/100952/21846/68169/108153/12832/12819/16998/58223/77739/56401/246228/320712/56429/14219/56693/58859/241327/237759/80883/233332/12389/12822/241226 |
| GO:0045229 | 61 | 0.1924290 | BP | 0 | 0 | 19.430998 | 0 | external encapsulating structure organization | 12814/16147/13078/17389/545370/20319/74199/20356/219151/12818/223838/94216/18214/70779/114249/208177/94214/271127/21810/23871/240322/14268/17390/15227/107581/14230/18073/320078/15117/268780/11504/12840/12817/50706/64075/16950/224697/18383/100952/21846/68169/108153/12832/12819/16998/58223/77739/56401/246228/320712/56429/14219/56693/58859/241327/237759/80883/233332/12389/12822/241226 |
| GO:0006816 | 68 | 0.1545455 | BP | 0 | 0 | 16.539232 | 0 | calcium ion transport | 338370/12288/20190/20730/319984/16000/11549/18127/20541/13491/13618/238384/320508/12293/17918/15894/14812/20855/18760/12766/20315/94249/12290/109676/110893/12310/270028/21838/22068/14612/12721/23796/381812/11607/13617/11517/16963/15558/66109/30948/217154/18763/81904/26903/65973/20192/74777/23832/56437/12523/58226/216869/19218/54598/14219/14360/18764/66972/68312/381290/317757/98660/14697/83408/12389/53376/12286/12298 |
| GO:0045785 | 70 | 0.1452282 | BP | 0 | 0 | 15.669697 | 0 | positive regulation of cell adhesion | 16147/13643/74199/140709/11600/16842/17242/16401/12522/16542/16000/114249/54371/12505/94214/18186/218952/23871/14268/15227/107581/15894/18073/21687/20315/15117/12554/268780/104709/14634/12310/27205/24099/21838/67916/12479/64075/12721/68606/16408/50931/14961/22341/20339/171285/20667/15002/100952/16002/68169/16963/18552/105855/14969/26903/320712/56349/14960/11492/20851/317757/22637/83408/58859/20443/54519/19242/16161/12389/16186 |
| GO:0034329 | 66 | 0.1496599 | BP | 0 | 0 | 15.400450 | 0 | cell junction assembly | 23888/14432/237979/22411/16542/235611/19266/20450/192167/13823/19277/208177/17475/18186/218952/12558/272381/12563/14268/107581/18164/17260/21687/56229/83964/210274/98733/54420/320873/330814/386750/12562/21838/67784/329165/13837/68606/245537/23796/69524/270163/73340/20401/269116/77569/11856/12552/50791/14615/18613/20613/13841/77446/219228/233651/50768/12741/70237/13048/53885/71228/236915/12389/12286/192897/12737 |
| GO:0031589 | 58 | 0.1554960 | BP | 0 | 0 | 14.093933 | 0 | cell-substrate adhesion | 19283/74199/140709/11600/17242/16401/16542/114249/208177/23928/94214/18186/218952/16421/14268/15227/107581/18073/21687/56229/15117/83964/12554/268780/109700/329872/12817/50706/21838/64075/12721/13837/68606/16408/77569/22341/11856/15434/208777/56363/100952/68169/18613/64099/16404/18552/170736/105298/50768/320712/56349/14219/58859/19242/80883/84544/241226/192897 |
| GO:0050808 | 67 | 0.1356275 | BP | 0 | 0 | 13.607371 | 0 | synapse organization | 23888/14432/237979/241568/235611/19266/20450/192167/19277/242662/55983/231602/18186/12558/272381/245880/66725/18164/17260/17918/18645/14812/210274/93706/98733/330814/327814/110893/386750/67784/210293/14658/16560/329165/68507/13837/245537/217480/73340/269116/442801/11816/260297/72333/13602/50791/232560/13841/238988/219228/70530/73181/14360/70237/13385/13048/18483/71228/240057/67790/53972/236915/19242/80883/59036/12286/12298 |
| GO:0048754 | 40 | 0.2083333 | BP | 0 | 0 | 13.607371 | 0 | branching morphogenesis of an epithelial tube | 16147/20319/20356/22420/11600/15245/11835/16842/17242/15431/16542/18121/16000/21385/114249/12505/15396/18186/271127/14734/11839/15227/21687/20315/14634/21412/238057/67784/17313/11607/69903/21386/21846/13617/18763/19206/233651/73181/329628/71228 |
| GO:0007224 | 36 | 0.2264151 | BP | 0 | 0 | 13.299057 | 0 | smoothened signaling pathway | 14632/16147/15245/68525/18121/19207/59056/16576/72507/14734/56297/15227/20720/68099/71492/94187/78795/14634/73916/218232/19376/216795/240888/18605/110350/15258/56350/67884/19206/234740/264134/140810/66573/19335/71228/71951 |
| GO:0098742 | 41 | 0.1915888 | BP | 0 | 0 | 12.724548 | 0 | cell-cell adhesion via plasma-membrane adhesion molecules | 23888/235472/545370/73173/237979/84004/16401/241568/19266/192167/12558/272381/12563/23965/13131/12554/93706/98733/320873/330814/386750/12562/279653/19274/53601/13837/69524/16408/72333/20339/13602/12552/50791/18613/219228/233651/270120/329628/80883/93885/12737 |
| GO:0001655 | 56 | 0.1447028 | BP | 0 | 0 | 12.381648 | 0 | urogenital system development | 20897/22420/11600/11835/22411/72135/15431/18121/13123/16000/114249/19277/12505/15396/18186/271127/14734/13618/66725/17390/15227/17260/15903/107587/18073/15904/21687/13809/14561/11504/14634/21412/14725/67784/243931/12142/12577/73692/18605/11607/56198/110350/13617/18552/55994/18763/13841/56350/19206/23967/233651/66333/18764/329628/71228/241226 |
| GO:0001667 | 61 | 0.1349558 | BP | 0 | 0 | 12.254700 | 0 | ameboidal-type cell migration | 13078/20356/11600/22411/16401/16542/16000/14026/20357/18214/24136/18127/20541/20361/18186/23871/12558/13618/16421/14268/17260/18645/19245/20855/18760/21687/20315/15117/12554/83397/13616/238328/12310/12562/67784/71709/67916/19274/16590/68606/240185/20401/72446/22341/11816/13617/16002/76441/18613/218877/17311/79221/381290/23797/14314/20358/11881/78560/212307/114886/192897 |
| GO:0034765 | 64 | 0.1285141 | BP | 0 | 0 | 11.981174 | 0 | regulation of ion transmembrane transport | 98741/338370/16519/329152/16494/12288/16508/56543/192167/77574/20541/399548/13491/20265/18301/226922/12293/17260/17918/18760/12766/12290/13616/109676/18795/21838/22068/110876/12721/245537/23796/381812/260297/11607/16531/99738/13617/66109/30948/217154/81904/26903/56461/14199/65973/74777/23967/56437/58226/66733/19218/14360/18764/20269/13385/68312/381290/98660/14697/18671/60613/12389/12286/12298 |
| GO:0001822 | 50 | 0.1515152 | BP | 0 | 0 | 11.769306 | 0 | kidney development | 20897/22420/11600/22411/72135/15431/18121/114249/19277/12505/15396/18186/271127/14734/13618/66725/17260/15903/107587/18073/21687/13809/14561/11504/14634/21412/14725/67784/243931/12142/12577/73692/18605/11607/56198/110350/13617/18552/55994/18763/13841/56350/19206/23967/233651/66333/18764/329628/71228/241226 |
| GO:0061138 | 41 | 0.1782609 | BP | 0 | 0 | 11.769306 | 0 | morphogenesis of a branching epithelium | 16147/15234/20319/20356/22420/11600/15245/11835/16842/17242/15431/16542/18121/16000/21385/114249/12505/15396/18186/271127/14734/11839/15227/21687/20315/14634/21412/238057/67784/17313/11607/69903/21386/21846/13617/18763/19206/233651/73181/329628/71228 |
| GO:0072001 | 51 | 0.1478261 | BP | 0 | 0 | 11.640055 | 0 | renal system development | 20897/22420/11600/22411/72135/15431/18121/114249/19277/12505/15396/18186/271127/14734/13618/66725/15227/17260/15903/107587/18073/21687/13809/14561/11504/14634/21412/14725/67784/243931/12142/12577/73692/18605/11607/56198/110350/13617/18552/55994/18763/13841/56350/19206/23967/233651/66333/18764/329628/71228/241226 |
| GO:0070588 | 47 | 0.1566667 | BP | 0 | 0 | 11.571788 | 0 | calcium ion transmembrane transport | 338370/12288/20190/20541/13491/13618/238384/12293/17918/14812/18760/12766/94249/12290/109676/110893/270028/21838/22068/12721/23796/381812/11607/13617/16963/15558/66109/30948/217154/18763/81904/26903/65973/20192/74777/23832/56437/19218/14360/18764/66972/68312/381290/98660/14697/12286/12298 |
| GO:0051924 | 45 | 0.1567944 | BP | 0 | 0 | 11.049668 | 0 | regulation of calcium ion transport | 12288/20730/319984/16000/18127/20541/13491/12293/17918/15894/20855/18760/12766/20315/109676/12310/21838/22068/12721/23796/381812/11607/13617/11517/66109/30948/217154/26903/65973/74777/56437/12523/216869/19218/14360/18764/68312/317757/98660/14697/83408/12389/53376/12286/12298 |
| GO:0060562 | 54 | 0.1367089 | BP | 0 | 0 | 11.049668 | 0 | epithelial tube morphogenesis | 16147/20319/20356/22420/11600/15245/11835/16842/17242/15431/16542/18121/16000/21385/24136/114249/12505/15396/18186/271127/14734/11839/15227/17260/21687/20315/14634/21412/14725/238057/73916/67784/330409/17313/23796/11607/69903/21386/21846/13617/106042/18763/13841/19206/69718/23967/233651/50768/73181/18764/57265/19335/329628/71228 |
| GO:0006874 | 62 | 0.1240000 | BP | 0 | 0 | 10.986671 | 0 | cellular calcium ion homeostasis | 16527/12288/20190/16542/11549/20541/231602/19309/51800/13618/238384/12293/17918/234515/14812/78134/20855/18760/12766/94249/12290/19220/13616/109676/110893/12310/12562/19228/270028/21838/22068/12721/23796/72844/14806/11816/12494/11607/13617/11517/12062/16963/15558/18763/65973/20192/74777/23832/19218/14360/18764/66972/57265/13385/68312/381290/317757/98660/83408/12389/12286/12298 |
| GO:0031345 | 38 | 0.1767442 | BP | 0 | 0 | 10.778939 | 0 | negative regulation of cell projection organization | 19283/13643/17756/20356/14026/20357/192167/20361/18186/121021/235106/13131/66725/66610/18645/14812/21838/22068/13837/209743/245537/244152/11816/12494/218877/19347/237847/13841/73181/18007/14360/270120/233781/22240/240057/20358/53972/74201 |
| GO:0010959 | 57 | 0.1278027 | BP | 0 | 0 | 10.548276 | 0 | regulation of metal ion transport | 329152/12288/20730/319984/16000/18127/20541/399548/13491/18301/12293/17918/15894/20855/20720/18760/12766/20315/13616/109676/12310/18795/21838/22068/12721/23796/381812/11607/13617/11517/15558/66109/30948/217154/26903/56461/14199/65973/74777/23967/56437/12523/216869/19218/14360/18764/68312/381290/317757/23797/98660/14697/83408/12389/53376/12286/12298 |
| GO:0060402 | 34 | 0.1899441 | BP | 0 | 0 | 10.437468 | 0 | calcium ion transport into cytosol | 12288/20190/11549/20541/238384/12293/17918/14812/18760/12766/12290/109676/110893/12310/270028/21838/12721/23796/11607/13617/11517/16963/15558/65973/20192/74777/23832/14360/18764/68312/317757/83408/12389/12286 |
| GO:0050673 | 59 | 0.1239496 | BP | 0 | 0 | 10.430508 | 0 | epithelial cell proliferation | 14632/16147/15234/20319/20356/11835/17242/16401/235505/16542/216439/18121/13123/16000/21385/68888/14313/14734/13618/11839/12444/17260/107587/18760/21687/12766/20315/15117/12554/238328/12310/73916/20913/19274/16590/228852/23796/12577/240185/22341/11816/11607/21846/13617/16002/16601/13345/26903/19206/23967/66333/30878/23797/353156/19242/12389/226841/16010/12737 |
| GO:0060401 | 36 | 0.1791045 | BP | 0 | 0 | 10.370789 | 0 | cytosolic calcium ion transport | 12288/20190/11549/20541/238384/12293/17918/14812/18760/12766/12290/109676/110893/12310/270028/21838/12721/23796/11607/13617/11517/16963/15558/65973/20192/74777/23832/14219/14360/18764/66972/68312/317757/83408/12389/12286 |
| GO:0003018 | 39 | 0.1659574 | BP | 0 | 0 | 10.276817 | 0 | vascular process in circulatory system | 11600/12288/16542/69219/11549/18127/20541/12411/18162/218952/13618/17390/15894/74682/19245/26357/83397/13616/109700/12310/12562/15551/19274/60596/11816/12494/11607/16531/13617/12062/15558/242202/12741/19218/30878/98660/18671/27405/12389 |
| GO:0048736 | 36 | 0.1764706 | BP | 0 | 0 | 10.213983 | 0 | appendage development | 16147/20319/16842/12288/15430/15431/18121/16764/106522/21385/225743/15396/218952/14734/15438/15395/107587/68099/71492/226844/14634/216795/64075/73692/18605/21386/110350/18552/15405/19206/234740/65973/23967/140810/19335/192897 |
| GO:0060173 | 36 | 0.1764706 | BP | 0 | 0 | 10.213983 | 0 | limb development | 16147/20319/16842/12288/15430/15431/18121/16764/106522/21385/225743/15396/218952/14734/15438/15395/107587/68099/71492/226844/14634/216795/64075/73692/18605/21386/110350/18552/15405/19206/234740/65973/23967/140810/19335/192897 |
| GO:0007409 | 59 | 0.1196755 | BP | 0 | 0 | 9.848769 | 0 | axonogenesis | 14432/13842/235472/19283/13643/17756/20356/26565/16401/241568/13176/18121/235611/14026/20357/225743/24136/19277/20361/18186/12558/14268/13131/18164/17260/20315/52666/13616/14634/14725/386750/238057/21838/67784/19274/17984/16773/13837/245537/17181/244152/269116/11816/12552/13617/218877/237847/18080/13841/246048/19206/18007/22253/381979/240057/20358/80883/68404/12286 |
Visualisation
bp_dot[[2]]
mf_dot[[2]]
cc_dot[[2]]
upset[[2]]
# display the top 30 most sig
enrichGO_sig[[3]][1:30, ] %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover")) %>%
scroll_box(height = "600px")| Count | GeneRatio | ontology | pvalue | p.adjust | logFDR | qvalue | Description | geneID | |
|---|---|---|---|---|---|---|---|---|---|
| GO:0048754 | 22 | 0.1145833 | BP | 0e+00 | 0.00e+00 | 12.242458 | 0.00e+00 | branching morphogenesis of an epithelial tube | 16147/22420/20319/15245/16842/11600/20356/17242/18121/21385/15431/271127/16000/11839/114249/16542/14734/15396/15227/12505/20315/238057 |
| GO:0061138 | 23 | 0.1000000 | BP | 0e+00 | 0.00e+00 | 11.925505 | 0.00e+00 | morphogenesis of a branching epithelium | 16147/15234/22420/20319/15245/16842/11600/20356/17242/18121/21385/15431/271127/16000/11839/114249/16542/14734/15396/15227/12505/20315/238057 |
| GO:0030198 | 24 | 0.0761905 | BP | 0e+00 | 0.00e+00 | 10.331034 | 0.00e+00 | extracellular matrix organization | 13078/16147/12814/545370/74199/17389/20319/20356/223838/12818/94216/271127/219151/114249/94214/70779/21810/15227/15117/12840/320078/240322/17390/18073 |
| GO:0043062 | 24 | 0.0759494 | BP | 0e+00 | 0.00e+00 | 10.331034 | 0.00e+00 | extracellular structure organization | 13078/16147/12814/545370/74199/17389/20319/20356/223838/12818/94216/271127/219151/114249/94214/70779/21810/15227/15117/12840/320078/240322/17390/18073 |
| GO:0045229 | 24 | 0.0757098 | BP | 0e+00 | 0.00e+00 | 10.331034 | 0.00e+00 | external encapsulating structure organization | 13078/16147/12814/545370/74199/17389/20319/20356/223838/12818/94216/271127/219151/114249/94214/70779/21810/15227/15117/12840/320078/240322/17390/18073 |
| GO:0097485 | 19 | 0.0733591 | BP | 0e+00 | 0.00e+00 | 7.598576 | 0.00e+00 | neuron projection guidance | 14432/13842/235472/13643/26565/20356/13176/18121/20357/19277/225743/235611/26757/13616/14725/14026/20361/20315/238057 |
| GO:0060562 | 23 | 0.0582278 | BP | 0e+00 | 0.00e+00 | 7.598576 | 0.00e+00 | epithelial tube morphogenesis | 16147/22420/20319/15245/16842/11600/20356/17242/18121/21385/15431/271127/16000/11839/114249/16542/14734/15396/15227/12505/14725/20315/238057 |
| GO:0007409 | 25 | 0.0507099 | BP | 0e+00 | 1.00e-07 | 7.219570 | 0.00e+00 | axonogenesis | 14432/13842/19283/235472/13643/17756/26565/20356/13176/18121/241568/20357/19277/225743/16401/235611/18164/12558/13131/13616/14725/14026/20361/20315/238057 |
| GO:0007411 | 18 | 0.0697674 | BP | 0e+00 | 1.00e-07 | 6.832217 | 1.00e-07 | axon guidance | 14432/13842/235472/13643/26565/20356/13176/18121/20357/19277/225743/235611/13616/14725/14026/20361/20315/238057 |
| GO:0035107 | 15 | 0.0862069 | BP | 0e+00 | 2.00e-07 | 6.705054 | 1.00e-07 | appendage morphogenesis | 16147/20319/16842/16764/18121/106522/15430/21385/15431/225743/14734/15396/15395/107587/15438 |
| GO:0035108 | 15 | 0.0862069 | BP | 0e+00 | 2.00e-07 | 6.705054 | 1.00e-07 | limb morphogenesis | 16147/20319/16842/16764/18121/106522/15430/21385/15431/225743/14734/15396/15395/107587/15438 |
| GO:0001655 | 21 | 0.0542636 | BP | 0e+00 | 4.00e-07 | 6.434024 | 3.00e-07 | urogenital system development | 20897/22420/22411/11600/18121/15431/271127/16000/19277/13123/114249/72135/13618/14734/15396/15227/12505/107587/14725/17390/18073 |
| GO:0098742 | 16 | 0.0747664 | BP | 0e+00 | 4.00e-07 | 6.434024 | 3.00e-07 | cell-cell adhesion via plasma-membrane adhesion molecules | 23888/235472/545370/237979/73173/241568/84004/192167/19266/16401/272381/12563/12558/13131/23965/320873 |
| GO:0050673 | 23 | 0.0483193 | BP | 0e+00 | 5.00e-07 | 6.295310 | 4.00e-07 | epithelial cell proliferation | 14632/16147/15234/20319/20356/235505/17242/18121/21385/68888/16000/14313/11839/16401/13123/16542/13618/14734/12310/107587/15117/20315/216439 |
| GO:0030326 | 13 | 0.0909091 | BP | 0e+00 | 1.00e-06 | 5.991717 | 7.00e-07 | embryonic limb morphogenesis | 16147/20319/16842/16764/18121/15430/21385/15431/14734/15396/15395/107587/15438 |
| GO:0035113 | 13 | 0.0909091 | BP | 0e+00 | 1.00e-06 | 5.991717 | 7.00e-07 | embryonic appendage morphogenesis | 16147/20319/16842/16764/18121/15430/21385/15431/14734/15396/15395/107587/15438 |
| GO:0048736 | 15 | 0.0735294 | BP | 0e+00 | 1.10e-06 | 5.952010 | 8.00e-07 | appendage development | 16147/20319/16842/16764/18121/106522/15430/21385/15431/225743/14734/15396/15395/107587/15438 |
| GO:0060173 | 15 | 0.0735294 | BP | 0e+00 | 1.10e-06 | 5.952010 | 8.00e-07 | limb development | 16147/20319/16842/16764/18121/106522/15430/21385/15431/225743/14734/15396/15395/107587/15438 |
| GO:0042391 | 22 | 0.0469083 | BP | 0e+00 | 1.50e-06 | 5.833219 | 1.10e-06 | regulation of membrane potential | 16527/338370/14805/16508/380785/56543/242662/11549/13491/399548/192167/238384/20265/268860/16542/108013/231602/14812/101772/51800/110893/14397 |
| GO:0001569 | 8 | 0.1777778 | BP | 0e+00 | 3.80e-06 | 5.418955 | 2.70e-06 | branching involved in blood vessel morphogenesis | 16147/20319/16842/11600/20356/17242/16542/20315 |
| GO:0031644 | 14 | 0.0721649 | BP | 0e+00 | 3.80e-06 | 5.418955 | 2.70e-06 | regulation of nervous system process | 15234/380785/13491/16000/192167/18164/268860/13618/108013/12310/18127/14812/245880/110893 |
| GO:0048705 | 16 | 0.0613027 | BP | 0e+00 | 3.80e-06 | 5.418955 | 2.70e-06 | skeletal system morphogenesis | 16147/12814/17389/20319/15245/18121/15430/15431/15396/20855/12411/107587/15117/15438/329872/17390 |
| GO:0009581 | 12 | 0.0875912 | BP | 0e+00 | 4.30e-06 | 5.365650 | 3.10e-06 | detection of external stimulus | 12814/20356/20357/16000/238384/20265/12310/15227/14812/20720/101772/20315 |
| GO:0072001 | 18 | 0.0521739 | BP | 0e+00 | 5.40e-06 | 5.269144 | 3.80e-06 | renal system development | 20897/22420/22411/11600/18121/15431/271127/19277/114249/72135/13618/14734/15396/15227/12505/107587/14725/18073 |
| GO:0003012 | 20 | 0.0465116 | BP | 0e+00 | 6.10e-06 | 5.217823 | 4.30e-06 | muscle system process | 56543/20190/12818/24052/11549/21385/399548/16000/20265/114249/109272/268860/13618/50876/20855/12310/18127/13616/231602/110893 |
| GO:0006936 | 17 | 0.0541401 | BP | 1e-07 | 7.00e-06 | 5.152796 | 5.00e-06 | muscle contraction | 56543/20190/24052/11549/21385/399548/20265/114249/109272/268860/13618/50876/20855/12310/13616/231602/110893 |
| GO:0001822 | 17 | 0.0515152 | BP | 1e-07 | 1.34e-05 | 4.872743 | 9.60e-06 | kidney development | 20897/22420/22411/11600/18121/15431/271127/19277/114249/72135/13618/14734/15396/12505/107587/14725/18073 |
| GO:0072006 | 12 | 0.0764331 | BP | 1e-07 | 1.50e-05 | 4.823193 | 1.07e-05 | nephron development | 22420/11600/18121/15431/271127/19277/114249/13618/14734/15396/12505/18073 |
| GO:0060348 | 15 | 0.0581395 | BP | 1e-07 | 1.50e-05 | 4.823193 | 1.07e-05 | bone development | 16147/17389/20319/20190/15431/16000/235611/16542/59056/15396/20855/12411/107587/15117/329872 |
| GO:0007224 | 12 | 0.0754717 | BP | 2e-07 | 1.63e-05 | 4.787675 | 1.17e-05 | smoothened signaling pathway | 14632/16147/15245/19207/18121/68525/59056/14734/15227/20720/72507/16576 |
Visualisation
bp_dot[[3]]
mf_dot[[3]]
cc_dot[[3]]
upset[[3]]
Export Data
# save to excel
writexl::write_xlsx(x = enrichGO_sig, here::here("3_output/enrichGO_sig.xlsx"))
saveRDS(object = enrichGO_sig,file = here::here("0_data/RDS_objects/enrichGO_sig.rds"))
saveRDS(object = enrichGO,file = here::here("0_data/RDS_objects/enrichGO.rds"))
sessionInfo()R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.utf8 LC_CTYPE=English_Australia.utf8
[3] LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Australia.utf8
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] enrichplot_1.16.2 org.Mm.eg.db_3.15.0 AnnotationDbi_1.58.0
[4] IRanges_2.30.1 S4Vectors_0.34.0 Biobase_2.56.0
[7] BiocGenerics_0.42.0 clusterProfiler_4.4.4 Glimma_2.6.0
[10] edgeR_3.38.4 limma_3.52.4 ggrepel_0.9.1
[13] ggbiplot_0.55 scales_1.2.1 plyr_1.8.7
[16] gridExtra_2.3 kableExtra_1.3.4 forcats_0.5.2
[19] stringr_1.4.1 purrr_0.3.5 tidyr_1.2.1
[22] ggplot2_3.3.6 tidyverse_1.3.2 reshape2_1.4.4
[25] tibble_3.1.8 readr_2.1.3 magrittr_2.0.3
[28] dplyr_1.0.10
loaded via a namespace (and not attached):
[1] utf8_1.2.2 tidyselect_1.2.0
[3] RSQLite_2.2.18 htmlwidgets_1.5.4
[5] BiocParallel_1.30.3 scatterpie_0.1.8
[7] munsell_0.5.0 codetools_0.2-18
[9] ragg_1.2.3 withr_2.5.0
[11] colorspace_2.0-3 GOSemSim_2.22.0
[13] highr_0.9 knitr_1.40
[15] rstudioapi_0.14 DOSE_3.22.1
[17] labeling_0.4.2 MatrixGenerics_1.8.1
[19] git2r_0.30.1 GenomeInfoDbData_1.2.8
[21] polyclip_1.10-0 bit64_4.0.5
[23] farver_2.1.1 rprojroot_2.0.3
[25] downloader_0.4 vctrs_0.4.2
[27] treeio_1.20.2 generics_0.1.3
[29] xfun_0.33 R6_2.5.1
[31] GenomeInfoDb_1.32.4 graphlayouts_0.8.2
[33] locfit_1.5-9.6 bitops_1.0-7
[35] cachem_1.0.6 fgsea_1.22.0
[37] gridGraphics_0.5-1 DelayedArray_0.22.0
[39] assertthat_0.2.1 promises_1.2.0.1
[41] ggraph_2.1.0 googlesheets4_1.0.1
[43] gtable_0.3.1 tidygraph_1.2.2
[45] workflowr_1.7.0 rlang_1.0.6
[47] genefilter_1.78.0 systemfonts_1.0.4
[49] splines_4.2.1 lazyeval_0.2.2
[51] gargle_1.2.1 broom_1.0.1
[53] yaml_2.3.5 modelr_0.1.9
[55] backports_1.4.1 httpuv_1.6.6
[57] qvalue_2.28.0 tools_4.2.1
[59] ggplotify_0.1.0 ellipsis_0.3.2
[61] jquerylib_0.1.4 RColorBrewer_1.1-3
[63] Rcpp_1.0.9 zlibbioc_1.42.0
[65] RCurl_1.98-1.9 viridis_0.6.2
[67] SummarizedExperiment_1.26.1 haven_2.5.1
[69] fs_1.5.2 here_1.0.1
[71] data.table_1.14.2 DO.db_2.9
[73] reprex_2.0.2 googledrive_2.0.0
[75] matrixStats_0.62.0 hms_1.1.2
[77] patchwork_1.1.2 evaluate_0.17
[79] xtable_1.8-4 XML_3.99-0.11
[81] readxl_1.4.1 ggupset_0.3.0
[83] compiler_4.2.1 writexl_1.4.0
[85] crayon_1.5.2 shadowtext_0.1.2
[87] htmltools_0.5.3 ggfun_0.0.7
[89] later_1.3.0 tzdb_0.3.0
[91] geneplotter_1.74.0 aplot_0.1.8
[93] lubridate_1.8.0 DBI_1.1.3
[95] tweenr_2.0.2 dbplyr_2.2.1
[97] MASS_7.3-57 Matrix_1.5-1
[99] cli_3.4.1 parallel_4.2.1
[101] igraph_1.3.5 GenomicRanges_1.48.0
[103] pkgconfig_2.0.3 xml2_1.3.3
[105] ggtree_3.4.4 svglite_2.1.0
[107] annotate_1.74.0 bslib_0.4.0
[109] webshot_0.5.4 XVector_0.36.0
[111] rvest_1.0.3 yulab.utils_0.0.5
[113] digest_0.6.29 Biostrings_2.64.1
[115] rmarkdown_2.17 cellranger_1.1.0
[117] fastmatch_1.1-3 tidytree_0.4.1
[119] lifecycle_1.0.3 nlme_3.1-157
[121] jsonlite_1.8.2 viridisLite_0.4.1
[123] fansi_1.0.3 pillar_1.8.1
[125] lattice_0.20-45 KEGGREST_1.36.3
[127] fastmap_1.1.0 httr_1.4.4
[129] survival_3.3-1 GO.db_3.15.0
[131] glue_1.6.2 png_0.1-7
[133] bit_4.0.4 ggforce_0.4.1
[135] stringi_1.7.8 sass_0.4.2
[137] blob_1.2.3 textshaping_0.3.6
[139] DESeq2_1.36.0 memoise_2.0.1
[141] ape_5.6-2