Gene ontology (GO) Analysis

Visualisations

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Last updated: 2024-02-08

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Knit directory: Treg_uNK/1_analysis/

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File	Version	Author	Date	Message
Rmd	8da2e31	tranmanhha135	2024-02-08	workflowr::wflow_publish(here::here("1_analysis/*.Rmd"))
html	36aeb85	Ha Manh Tran	2024-01-13	Build site.
Rmd	c78dfac	tranmanhha135	2024-01-12	remote from ipad
html	c78dfac	tranmanhha135	2024-01-12	remote from ipad
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Rmd	221e2fa	tranmanhha135	2024-01-10	fixed error
html	221e2fa	tranmanhha135	2024-01-10	fixed error
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Rmd	05fa0b3	tranmanhha135	2024-01-06	added description

# working with data
library(dplyr)
library(magrittr)
library(readr)
library(tibble)
library(reshape2)
library(tidyverse)

# Visualisation:
library(kableExtra)
library(ggplot2)
library(grid)
library(DT)
library(extrafont)
library(VennDiagram)
# Custom ggplot
library(gridExtra)
library(ggbiplot)
library(ggrepel)
library(rrvgo)
library(d3treeR)
library(plotly)
library(GOSemSim)
library(data.table)

# Bioconductor packages:
library(edgeR)
library(limma)
library(Glimma)
library(clusterProfiler)
library(org.Mm.eg.db)
library(enrichplot)
library(patchwork)

library(pandoc)
library(knitr)
opts_knit$set(progress = FALSE, verbose = FALSE)
opts_chunk$set(warning=FALSE, message=FALSE, echo=FALSE)

Gene ontology (GO) Analysis

Functional enrichment analysis is a method used to identify biological functions or processes overrepresented in a set of genes or proteins.

Gene Ontology (GO) is a standardized system for annotating genes and their products with terms from a controlled vocabulary, organized into three main categories: Molecular Function, Biological Process, and Cellular Component.

Biological Process (BP): Describes the larger, coordinated biological events or processes in which a gene product is involved. This category represents a series of molecular events that contribute to a specific function.
Molecular Function (MF): Describes the specific molecular activities that a gene product performs, such as catalytic or binding activities.
Cellular Component (CC): Describes the location or structure within the cell where a gene product is active, such as the nucleus, cytoplasm, or membrane.

Each of these three main categories is further organized into a hierarchical structure with more specific terms. The terms become more specialized as you move down the hierarchy (ontology level). Comparing a gene list to a reference database offers critical insights into the biological significance of gene expression changes.

Visualisations

The following visualisations are GO enrichment analysis performed with set of DE genes significantly below FDR 0.1 without FC threshold (TREAT). IMPORTANTLY, these GO terms are all significantly enriched (FDR <0.05)

Dot plot: illustrates the top 25 enriched GO terms.
- $Gene ratio =$ the number of significant DE gene in the term / the total of number of genes in the term. Indicated by the size
- The shapes represents the three main GO categories, either BP, MP, or CC
Table: list of all the significant GO terms
Upset: illustrate the overlap of gene between different functional terms

Semantic similarity plots - GO specific

Due to the hierarchical structure of Gene Ontologies, the enriched sets generated often exhibit redundancy and pose challenges in interpretation. The subsequent analyses and visualizations seek to alleviate this redundancy in GO sets by grouping comparable terms based on their semantic similarity. The underlying concept behind measuring semantic similarity is grounded in the idea that genes sharing similar functions should possess analogous annotation vocabulary and exhibit close relationships within the ontology structure.

NOTE: the following semantic similarity analyses are performed using Graph-based method (Wang et al. 2007)

Dendrogram plot: performs hierarchical clustering on the semantic similarity of GO terms.
- NOTE: to maintain readability, only the top 50 most significant GO terms are clustered. These clusters are then divided into 9 clades and labeled using the top 4 high-frequency words.
Scatter plot: illustrates the UMAP space between semantically similar significant GO terms
- Distances represent the similarity between terms,
- Size represents the significance (in $-\log_{10}FDR$ ))
- NOTE: to maintain reability, only the top 15 most significant parent terms are labeled. Parent terms are the most significant term in a particular cluster
Treemap plot: Visualise the of hierarchical structures of semantically similar GO terms.
- The terms are colored based on their parent term,
- The size of the term is proportional to the significance.

I recommend reading through the full list of significant GO terms and selecting the most biologically relevant for better visualisation

Version	Author	Date
c78dfac	tranmanhha135	2024-01-12
221e2fa	tranmanhha135	2024-01-10
762020e	tranmanhha135	2024-01-09

Show entries

Search:

	ONTOLOGY	ID	Description	GeneRatio	Total	Universe	pvalue	p.adjust	qvalue	geneID	Count	shortest_path	longest_path	terminal_node	ontology	logFDR
GO:0002449	BP	GO:0002449	Lymphocyte mediated immunity	0.131	244	13445	4.27e-12	1.73e-08	1.5e-08	H2-Q4/Tap1/B2m/H2-K1/C2/Gzmf/Tap2/H2-D1/Serping1/Parp3/Nfkbiz/Cd55/Gzmd/Il31ra/Serpinb9/C1s1/Ccr2/Irf7/H2-T23/Gzme/Il2rb/Gzmc/Gzmg/Ctsc/Icam1/Ptprc/Havcr2/Spn/Lamp1/C1ra/Gzmb/Prf1	32	4	4	false	BP	7.76
GO:0002443	BP	GO:0002443	Leukocyte mediated immunity	0.113	328	13445	8.59e-12	1.74e-08	1.51e-08	H2-Q4/Tap1/B2m/H2-K1/C2/Gzmf/Tap2/H2-D1/Serping1/Parp3/Nfkbiz/Cd55/Gzmd/Anxa3/Il31ra/Serpinb9/C1s1/Ccr2/Irf7/H2-T23/Gzme/Il2rb/Ctsg/Gzmc/Gzmg/Ctsc/Icam1/Ptprc/Havcr2/Spn/Itgb2l/Lamp1/C1ra/Rac2/Ptgdr/Gzmb/Prf1	37	3	3	false	BP	7.76
GO:0140507	BP	GO:0140507	Granzyme-mediated programmed cell death signaling pathway	0.643	14	13445	4.16e-11	5.62e-08	4.89e-08	Gzmf/Gzmd/Srgn/Gzme/Gzmc/Gzmg/Lamp1/Gzmb/Prf1	9					7.25
GO:0001906	BP	GO:0001906	Cell killing	0.162	142	13445	6.62e-11	6.69e-08	5.82e-08	H2-Q4/Tap1/B2m/H2-K1/Gzmf/Tap2/H2-D1/Kng2/Cd55/Gzmd/Serpinb9/H2-T23/Gzme/Ctsg/Gzmc/Gzmg/Ctsc/Ptprc/Havcr2/Lamp1/Bcl2l11/Gzmb/Prf1	23	2	2	false	BP	7.17
GO:0001909	BP	GO:0001909	Leukocyte mediated cytotoxicity	0.187	107	13445	8.27e-11	6.69e-08	5.82e-08	H2-Q4/Tap1/B2m/H2-K1/Gzmf/Tap2/H2-D1/Gzmd/Serpinb9/H2-T23/Gzme/Ctsg/Gzmc/Gzmg/Ctsc/Ptprc/Havcr2/Lamp1/Gzmb/Prf1	20	3	4	false	BP	7.17
GO:0035458	BP	GO:0035458	Cellular response to interferon-beta	0.286	42	13445	3.14e-09	2.11e-06	1.84e-06	Iigp1/Gbp2/Stat1/Tgtp2/Gbp3/Irgm2/Irgm1/Gbp6/Oas1a/Ifi47/Gm12185/Tgtp1	12	6	6	true	BP	5.67
GO:0002456	BP	GO:0002456	T cell mediated immunity	0.173	98	13445	7.23e-09	4.18e-06	3.64e-06	H2-Q4/B2m/H2-K1/Tap2/H2-D1/Nfkbiz/Cd55/Il31ra/Serpinb9/Ccr2/H2-T23/Ctsc/Icam1/Ptprc/Spn/Gzmb/Prf1	17	5	5	false	BP	5.38
GO:0002250	BP	GO:0002250	Adaptive immune response	0.0954	346	13445	9.08e-09	4.59e-06	4e-06	H2-Q4/Tap1/B2m/H2-K1/C2/Tap2/H2-D1/Serping1/Parp3/Zap70/Nfkbiz/Cd55/Il31ra/Serpinb9/C1s1/Ccr2/Irf7/H2-T23/Il2rb/Loxl3/Ctsc/Icam1/Ptprc/Havcr2/Serpina3g/Ly9/Spn/Lax1/C1ra/Eomes/Fcamr/Gzmb/Prf1	33	3	3	false	BP	5.34
GO:0042742	BP	GO:0042742	Defense response to bacterium	0.126	183	13445	1.09e-08	4.91e-06	4.28e-06	B2m/Iigp1/H2-K1/Gbp2/Irf8/Oas2/Lbp/Nfkbiz/Gbp4/Gbp8/Anxa3/Serpinb9/Gbp3/Ppl/Ctsg/Havcr2/Irgm2/Irgm1/Gbp6/Oas1a/Spn/Sftpd/Gzmb	23	4	6	false	BP	5.31
GO:0001913	BP	GO:0001913	T cell mediated cytotoxicity	0.282	39	13445	1.67e-08	6.77e-06	5.9e-06	H2-Q4/B2m/H2-K1/Tap2/H2-D1/Serpinb9/H2-T23/Ctsc/Ptprc/Gzmb/Prf1	11	4	6	false	BP	5.17

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Interactive scatter

3D Interactive scatter

[[1]]

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c78dfac	tranmanhha135	2024-01-12
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Interactive Tree

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c78dfac	tranmanhha135	2024-01-12
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.pl

Version	Author	Date
c78dfac	tranmanhha135	2024-01-12
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	ONTOLOGY	ID	Description	GeneRatio	Total	Universe	pvalue	p.adjust	qvalue	geneID	Count	shortest_path	longest_path	terminal_node	ontology	logFDR
GO:0006814	BP	GO:0006814	Sodium ion transport	0.175	177	13445	1.7e-09	8.01e-06	7.43e-06	Ednrb/Slc6a2/Kcnk1/Prss8/Drd4/Kcnq1/Chp1/Slc34a2/Slc6a14/Slc5a9/Rangrf/Atp12a/Scnn1b/Umod/Slc28a3/Hcn4/Kcnj1/Slc5a8/Slc9a2/Slc24a1/Slc17a1/Wnk2/Fgf14/Dmpk/Nos3/Slc13a1/Slc24a3/Guca2b/Slc5a3/Asic1/Slc24a5	31	7	7	false	BP	5.1
GO:0030855	BP	GO:0030855	Epithelial cell differentiation	0.117	488	13445	4.91e-09	1.15e-05	1.07e-05	Spint2/Xbp1/Tgfb2/Krt7/Krt19/Ppl/St14/Ezr/Pax8/Vdr/Cldn3/Grhl2/Ednrb/Cdh1/Nfkbiz/Bhlha15/Strc/Fat1/Abcb1b/Il31ra/Dlx5/Nkx6-3/Mycn/Kcnq1/Pax2/Esrp1/Elf3/Gsdme/Krt17/Met/Hnf1b/Ehf/Pdpn/Fgfr2/Pck1/Kdf1/Dact2/Cd24a/Fam20c/Krt80/Prom1/Syne4/Scrib/Lor/Rilpl1/Zfp703/Shroom3/Irf6/Cgn/Cdk6/Rab25/Stat5a/Sall1/Whrn/Cyp26b1/Skil/Krt84	57	4	5	false	BP	4.94
GO:0072044	BP	GO:0072044	Collecting duct development	0.7	10	13445	9.73e-08	0.000153	0.000141	Pax8/Pax2/Dact2/Wnt7b/Umod/Spp1/Aqp2	7	4	8	false	BP	3.82
GO:0003382	BP	GO:0003382	Epithelial cell morphogenesis	0.308	39	13445	3.4e-07	4e-04	0.000371	Spint2/St14/Cldn3/Grhl2/Cdh1/Fat1/Met/Dact2/Scrib/Rilpl1/Cgn/Rab25	12	5	7	false	BP	3.4
GO:0002009	BP	GO:0002009	Morphogenesis of an epithelium	0.107	478	13445	5.75e-07	0.000541	0.000501	Spint2/Tgfb2/Casr/Spint1/St14/Pax8/Vdr/Grhl2/Csf1/Cdh1/Esrp2/Fat1/Sulf1/Mycn/Lama3/Pax2/Lrg1/Esrp1/Krt17/Met/Hnf1b/Tgm2/Pdpn/Fgfr2/Cited2/Nog/Kdf1/Scnn1b/Wnt7b/Tgfbr2/Ddr1/Syne4/Fermt1/Scrib/Nphp1/Shroom3/Plet1/Lrp2/Lcn2/Stat5a/Enah/Cobl/Sema3c/Sfrp1/Sall1/Ripk4/Dchs1/Dact1/Hoxd11/Ift172/Npnt	51	4	5	false	BP	3.27
GO:0061138	BP	GO:0061138	Morphogenesis of a branching epithelium	0.141	191	13445	1.69e-06	0.00132	0.00123	Spint2/Casr/Spint1/St14/Pax8/Vdr/Grhl2/Csf1/Cdh1/Esrp2/Sulf1/Mycn/Pax2/Esrp1/Met/Hnf1b/Tgm2/Fgfr2/Nog/Tgfbr2/Ddr1/Sema3c/Sfrp1/Sall1/Dchs1/Hoxd11/Npnt	27	3	6	false	BP	2.88
GO:0001763	BP	GO:0001763	Morphogenesis of a branching structure	0.137	204	13445	1.97e-06	0.00133	0.00123	Spint2/Casr/Spint1/St14/Pax8/Vdr/Grhl2/Csf1/Cdh1/Esrp2/Sulf1/Mycn/Pax2/Esrp1/Met/Hnf1b/Tgm2/Fgfr2/Nog/Tgfbr2/Ddr1/Sema3c/Sfrp1/Sall1/Cpe/Dchs1/Hoxd11/Npnt	28	2	4	false	BP	2.88
GO:0008544	BP	GO:0008544	Epidermis development	0.126	254	13445	2.5e-06	0.00147	0.00136	Tgfb2/Krt7/Spint1/Ppl/St14/Vdr/Grhl2/Cdh1/Nfkbiz/Strc/Prss8/Tmprss13/Mycn/Kcnq1/Esrp1/Gsdme/Krt17/Met/Fgfr2/Kdf1/Barx2/Krt80/Fermt1/Scrib/Lor/Nab2/Irf6/Gab1/Whrn/Cyp26b1/Ift172/Krt84	32	4	4	false	BP	2.83
GO:0003014	BP	GO:0003014	Renal system process	0.183	93	13445	4.49e-06	0.00235	0.00218	Ednrb/Trpv5/Sulf1/Hsd11b2/Kcnq1/Rhpn2/Atp6v0a4/Kirrel/Scnn1b/Umod/Kcnj1/Wfs1/Aqp2/Ptger3/Guca2b/Slc25a23/Cln3	17	3	3	false	BP	2.63
GO:0035725	BP	GO:0035725	Sodium ion transmembrane transport	0.164	116	13445	6.78e-06	0.0027	0.0025	Slc6a2/Kcnk1/Prss8/Drd4/Kcnq1/Chp1/Slc6a14/Rangrf/Atp12a/Scnn1b/Slc28a3/Hcn4/Slc9a2/Slc24a1/Wnk2/Fgf14/Slc24a3/Asic1/Slc24a5	19	6	8	false	BP	2.57

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Interactive Scatter

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3D scatter

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.pl

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interactive_treemap(reducedTerms[[1]][[i]])

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	ONTOLOGY	ID	Description	GeneRatio	Total	Universe	pvalue	p.adjust	qvalue	geneID	Count	shortest_path	longest_path	terminal_node	ontology	logFDR
GO:0140507	BP	GO:0140507	Granzyme-mediated programmed cell death signaling pathway	0.429	14	13445	7.86e-10	1.48e-06	1.42e-06	Gzmf/Gzmg/Lamp1/Gzmd/Gzme/Gzmc	6					5.83
GO:0001909	BP	GO:0001909	Leukocyte mediated cytotoxicity	0.0935	107	13445	1.76e-08	1.49e-05	1.43e-05	H2-K1/B2m/Gzmf/Gzmg/Lamp1/H2-D1/Gzmd/H2-T23/Gzme/Gzmc	10	3	4	false	BP	4.83
GO:0001906	BP	GO:0001906	Cell killing	0.0775	142	13445	2.37e-08	1.49e-05	1.43e-05	H2-K1/B2m/Gzmf/Gzmg/Lamp1/H2-D1/Gzmd/H2-T23/Gzme/Gzmc/Ccl1	11	2	2	false	BP	4.83
GO:0019835	BP	GO:0019835	Cytolysis	0.333	15	13445	9.85e-08	4.63e-05	4.44e-05	Gzmf/Gzmg/Gzmd/Gzme/Gzmc	5	2	2	false	BP	4.33
GO:0002449	BP	GO:0002449	Lymphocyte mediated immunity	0.0492	244	13445	7.85e-07	0.000295	0.000283	H2-K1/B2m/Gzmf/Gzmg/Lamp1/H2-D1/Gzmd/C2/H2-T23/Gzme/Gzmc/Paxip1	12	4	4	false	BP	3.53
GO:0002428	BP	GO:0002428	Antigen processing and presentation of peptide antigen via MHC class Ib	0.333	12	13445	2.07e-06	0.000649	0.000622	H2-K1/B2m/H2-D1/H2-T23	4	4	4	false	BP	3.19
GO:0070269	BP	GO:0070269	Pyroptosis	0.185	27	13445	2.45e-06	0.000657	0.000631	Gzmf/Gzmg/Gzmd/Gzme/Gzmc	5	4	4	true	BP	3.18
GO:0042832	BP	GO:0042832	Defense response to protozoan	0.161	31	13445	5.02e-06	0.00117	0.00112	Gbp4/Iigp1/Gbp3/Gbp6/Irf8	5	4	6	false	BP	2.93
GO:0002475	BP	GO:0002475	Antigen processing and presentation via MHC class Ib	0.267	15	13445	5.6e-06	0.00117	0.00112	H2-K1/B2m/H2-D1/H2-T23	4	3	3	false	BP	2.93
GO:0002483	BP	GO:0002483	Antigen processing and presentation of endogenous peptide antigen	0.25	16	13445	7.42e-06	0.00126	0.00121	H2-K1/B2m/H2-D1/H2-T23	4	4	4	false	BP	2.9

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Version	Author	Date
c78dfac	tranmanhha135	2024-01-12
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.pl

Version	Author	Date
c78dfac	tranmanhha135	2024-01-12
221e2fa	tranmanhha135	2024-01-10
762020e	tranmanhha135	2024-01-09

Interactive Scatter

.pl

3D scatter

.pl

.pl

Version	Author	Date
c78dfac	tranmanhha135	2024-01-12
221e2fa	tranmanhha135	2024-01-10

interactive_treemap(reducedTerms[[1]][[i]])

Version	Author	Date
c78dfac	tranmanhha135	2024-01-12
221e2fa	tranmanhha135	2024-01-10
762020e	tranmanhha135	2024-01-09

Version	Author	Date
c78dfac	tranmanhha135	2024-01-12
221e2fa	tranmanhha135	2024-01-10

NULL

Biological Processes parent terms

Molecular Functions parent terms

Cellular Components parent terms

Biological processes parent terms

Version	Author	Date
c78dfac	tranmanhha135	2024-01-12
221e2fa	tranmanhha135	2024-01-10

Export Data

The following are exported:

GO.xlsx - This spreadsheet contains all significantly enriched GO terms. NOTE:

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

time zone: Australia/Adelaide
tzcode source: system (glibc)

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

other attached packages:
 [1] htmltools_0.5.7       knitr_1.45            pandoc_0.2.0         
 [4] patchwork_1.1.3       enrichplot_1.20.3     org.Mm.eg.db_3.17.0  
 [7] AnnotationDbi_1.62.2  IRanges_2.34.1        S4Vectors_0.38.2     
[10] Biobase_2.60.0        BiocGenerics_0.46.0   clusterProfiler_4.8.3
[13] Glimma_2.10.0         edgeR_3.42.4          limma_3.56.2         
[16] data.table_1.14.10    GOSemSim_2.26.1       plotly_4.10.3        
[19] d3treeR_0.1           rrvgo_1.12.2          ggrepel_0.9.4        
[22] ggbiplot_0.55         scales_1.3.0          plyr_1.8.9           
[25] gridExtra_2.3         VennDiagram_1.7.3     futile.logger_1.4.3  
[28] extrafont_0.19        DT_0.31               kableExtra_1.3.4     
[31] lubridate_1.9.3       forcats_1.0.0         stringr_1.5.1        
[34] purrr_1.0.2           tidyr_1.3.0           ggplot2_3.4.4        
[37] tidyverse_2.0.0       reshape2_1.4.4        tibble_3.2.1         
[40] readr_2.1.4           magrittr_2.0.3        dplyr_1.1.4          

loaded via a namespace (and not attached):
  [1] splines_4.3.2               later_1.3.2                
  [3] ggplotify_0.1.2             bitops_1.0-7               
  [5] polyclip_1.10-6             XML_3.99-0.16              
  [7] lifecycle_1.0.4             rprojroot_2.0.4            
  [9] MASS_7.3-60                 NLP_0.2-1                  
 [11] lattice_0.22-5              crosstalk_1.2.1            
 [13] sass_0.4.8                  rmarkdown_2.25             
 [15] jquerylib_0.1.4             yaml_2.3.8                 
 [17] httpuv_1.6.13               askpass_1.2.0              
 [19] reticulate_1.34.0           cowplot_1.1.2              
 [21] DBI_1.2.0                   RColorBrewer_1.1-3         
 [23] abind_1.4-5                 zlibbioc_1.46.0            
 [25] rvest_1.0.3                 GenomicRanges_1.52.1       
 [27] ggraph_2.1.0                RCurl_1.98-1.13            
 [29] yulab.utils_0.1.2           rappdirs_0.3.3             
 [31] tweenr_2.0.2                git2r_0.33.0               
 [33] GenomeInfoDbData_1.2.10     data.tree_1.1.0            
 [35] tm_0.7-11                   tidytree_0.4.6             
 [37] pheatmap_1.0.12             umap_0.2.10.0              
 [39] RSpectra_0.16-1             svglite_2.1.3              
 [41] gridSVG_1.7-5               codetools_0.2-19           
 [43] DelayedArray_0.26.7         ggforce_0.4.1              
 [45] DOSE_3.26.2                 xml2_1.3.6                 
 [47] tidyselect_1.2.0            aplot_0.2.2                
 [49] farver_2.1.1                viridis_0.6.4              
 [51] matrixStats_1.2.0           webshot_0.5.5              
 [53] jsonlite_1.8.8              ellipsis_0.3.2             
 [55] tidygraph_1.3.0             systemfonts_1.0.5          
 [57] ggnewscale_0.4.9            tools_4.3.2                
 [59] ragg_1.2.7                  treeio_1.24.3              
 [61] Rcpp_1.0.11                 glue_1.6.2                 
 [63] Rttf2pt1_1.3.12             here_1.0.1                 
 [65] xfun_0.41                   DESeq2_1.40.2              
 [67] qvalue_2.32.0               MatrixGenerics_1.12.3      
 [69] GenomeInfoDb_1.36.4         withr_2.5.2                
 [71] formatR_1.14                fastmap_1.1.1              
 [73] ggh4x_0.2.7                 fansi_1.0.6                
 [75] openssl_2.1.1               digest_0.6.33              
 [77] gridGraphics_0.5-1          timechange_0.2.0           
 [79] R6_2.5.1                    mime_0.12                  
 [81] textshaping_0.3.7           colorspace_2.1-0           
 [83] GO.db_3.17.0                RSQLite_2.3.4              
 [85] utf8_1.2.4                  generics_0.1.3             
 [87] graphlayouts_1.0.2          httr_1.4.7                 
 [89] htmlwidgets_1.6.4           S4Arrays_1.0.6             
 [91] scatterpie_0.2.1            whisker_0.4.1              
 [93] pkgconfig_2.0.3             gtable_0.3.4               
 [95] blob_1.2.4                  workflowr_1.7.1            
 [97] XVector_0.40.0              shadowtext_0.1.2           
 [99] fgsea_1.26.0                ggupset_0.3.0              
[101] png_0.1-8                   wordcloud_2.6              
[103] ggfun_0.1.3                 lambda.r_1.2.4             
[105] rstudioapi_0.15.0           tzdb_0.4.0                 
[107] nlme_3.1-163                cachem_1.0.8               
[109] parallel_4.3.2              HDO.db_0.99.1              
[111] treemap_2.4-4               pillar_1.9.0               
[113] vctrs_0.6.5                 slam_0.1-50                
[115] promises_1.2.1              xtable_1.8-4               
[117] extrafontdb_1.0             evaluate_0.23              
[119] cli_3.6.2                   locfit_1.5-9.8             
[121] compiler_4.3.2              futile.options_1.0.1       
[123] rlang_1.1.2                 crayon_1.5.2               
[125] labeling_0.4.3              fs_1.6.3                   
[127] writexl_1.4.2               stringi_1.8.3              
[129] viridisLite_0.4.2           gridBase_0.4-7             
[131] BiocParallel_1.34.2         munsell_0.5.0              
[133] Biostrings_2.68.1           lazyeval_0.2.2             
[135] Matrix_1.6-3                hms_1.1.3                  
[137] bit64_4.0.5                 KEGGREST_1.40.1            
[139] shiny_1.8.0                 highr_0.10                 
[141] SummarizedExperiment_1.30.2 igraph_1.6.0               
[143] memoise_2.0.1               bslib_0.6.1                
[145] ggtree_3.8.2                fastmatch_1.1-4            
[147] bit_4.0.5                   downloader_0.4             
[149] gson_0.1.0                  ape_5.7-1

Gene ontology (GO) analysis

Ha M. Tran

08-01-2024

Gene ontology (GO) Analysis

Visualisations

Export Data