Does enrichGO support “ENSEMBL” format?

[TianGong9]

Hello,
I am a beginner of bioinformatics and am using enrichGO to analyze up-regulated genes in tomato. My genes are in ensemble format (e.g. Solyc01g005730.3), but when I run

GO_results <-

• enrichGO(gene = Up_Genes,

•        OrgDb = org.Slycopersicum.eg.db,
  

•        keyType = 'ENSEMBL',ont="BP", readable=T)
  

It says: Error in get_GO_data(OrgDb, ont, keyType) : keytype is not supported...
But, based on this website: https://guangchuangyu.github.io/2016/01/go-analysis-using-clusterprofiler/, my gene format should work. Can anyone please help?
I also tried to convert it to different format using the following code whichcauses great loss of information.

transId(

• id = Up_Genes,
• transTo = c("entrez", "ensembl","symbol"), org = "slycopersicum", keepNA = TRUE
• )
  Some ID occurs one-to-many match, like "Solyc01g059965.1"

44.67% genes are mapped to entrezid
100% genes are mapped to ensembl
2.33% genes are mapped to symbol
Any thoughts or suggestions would be greatly appreciated!
Thank you!

[huerqiang]

Please use the latest version of clusterProfiler and get the document by ?enrichGO.

[guidohooiveld]

It has been a while that you posted this question, but since your genes are in ENSEMBL-format: why then not use the available GO annotations from ENSEMBL in combination with the generic function enrichr?

Below some example code for tomato that I adapted from one of my 'plant projects'. Also: some code snippets from this book chapter gave me a kick-start for the biomaRt code for plants.
https://pubmed.ncbi.nlm.nih.gov/35037199/

> library(biomaRt)
> 
> ## PART 1: check available plant marts
> listMarts( host="https://plants.ensembl.org" )
            biomart                      version
1       plants_mart      Ensembl Plants Genes 56
2 plants_variations Ensembl Plants Variations 56
> 
> ## connect to the mart database
> EPgenes = useEnsembl(biomart="plants_mart",  host="https://plants.ensembl.org")
> 
> ## find names of available plant data sets
> dsets = listDatasets(EPgenes)
> 
> head(dsets)
               dataset                                 description
1      aalpina_eg_gene           Arabis alpina genes (A_alpina_V4)
2   achinensis_eg_gene Actinidia chinensis genes (Red5_PS1_1.69.0)
3     acomosus_eg_gene                 Ananas comosus genes (F153)
4     ahalleri_eg_gene         Arabidopsis halleri genes (Ahal2.2)
5      alyrata_eg_gene            Arabidopsis lyrata genes (v.1.0)
6 aofficinalis_eg_gene      Asparagus officinalis genes (Aspof.V1)
          version
1     A_alpina_V4
2 Red5_PS1_1.69.0
3            F153
4         Ahal2.2
5           v.1.0
6        Aspof.V1
> 
> ## in this case, find the tomato one
> dsets[grep("Solanum lycopersicum", dsets$description),]
                  dataset                        description version
100 slycopersicum_eg_gene Solanum lycopersicum genes (SL3.0)   SL3.0
> 
> ## take a note of the dataset name 'slycopersicum_eg_gene'
> 
> 
> 
> ## PART 2: check available filters and attributes
> EPgenes = useMart( 
+ biomart="plants_mart",
+   host="https://plants.ensembl.org",
+ dataset="slycopersicum_eg_gene")
> 
> 
> head( listFilters(EPgenes) )
             name              description
1 chromosome_name Chromosome/scaffold name
2           start                    Start
3             end                      End
4      band_start               Band Start
5        band_end                 Band End
6    marker_start             Marker Start
> 
> 
> head( listAttributes(EPgenes) )
                   name              description         page
1       ensembl_gene_id           Gene stable ID feature_page
2 ensembl_transcript_id     Transcript stable ID feature_page
3    ensembl_peptide_id        Protein stable ID feature_page
4       ensembl_exon_id           Exon stable ID feature_page
5           description         Gene description feature_page
6       chromosome_name Chromosome/scaffold name feature_page
> 
> 
> 
> ## PART 3: download GO terms associated to all genes,
> ## and add name of terms ("name_1006") and ontologies ("namespace_1003")
> ## note genes might have duplicated entries
> go.all = getBM(attributes=c("ensembl_gene_id", "go_id", "name_1006", "namespace_1003"), 
+            mart=EPgenes) 
> 
> head(go.all)
   ensembl_gene_id      go_id                      name_1006     namespace_1003
1 Solyc12g042120.2                                                             
2 Solyc01g067380.3 GO:0006629        lipid metabolic process biological_process
3 Solyc05g006260.1                                                             
4 Solyc12g019340.1 GO:0016021 integral component of membrane cellular_component
5 Solyc12g097070.2 GO:0040008           regulation of growth biological_process
6 Solyc05g015710.3 GO:0016021 integral component of membrane cellular_component
> 
> dim(go.all)
[1] 96756     4
> 
> ## To get a feeling about the GO annotations:
> ## check how many of the 96756 entries have a GO annotation
> ## --> 82661
> sum(go.all$go_id != "")
[1] 82661
> 
> 
> ## check how many unique genes are represented in the 96756 entries?
> ## --> 35825
> sum(!duplicated( go.all$ensembl_gene_id) )
[1] 35825
> 
> 
> 
> ## remove the genes that don't have a GO annotation.
> go.all <- go.all[go.all$go_id != "", ]
> 
> dim(go.all)
[1] 82661     4
> 
> ## check how many unique genes are represented in the 82661 entries?
> ## --> 21730
> sum(!duplicated( go.all$ensembl_gene_id) )
[1] 21730
> 
> ## now perform GO overrepresentation analysis (ORA)
> ## for this randomly select 750 genes 
> 
> genes.random <- base::sample(go.all$ensembl_gene_id, 750)
> 
> head(genes.random)
[1] "Solyc08g082580.3" "Solyc12g095850.2" "Solyc04g079730.1" "Solyc04g064500.3"
[5] "Solyc06g073870.3" "Solyc02g089175.1"
> 
> 
>

[guidohooiveld]

example code continued.

> # PART 4: perform GO ORA analysis using all 3 ontologies
> # note the use of arguments TERM2GENE and TERM2NAME. Their column
> # order is important!
> # also: to show proof-of-principle no cutoff on significance
> # is applied! i.e Cutoff=1
> 
> library(clusterProfiler)
> 
> res.GO.ora <- enricher(
+     gene=genes.random,
+     pvalueCutoff = 1,
+     pAdjustMethod = "none",
+     universe=go.all$ensembl_gene_id,
+     minGSSize = 10,
+     maxGSSize = 500,
+     qvalueCutoff = 1,
+     TERM2GENE = go.all[ ,c("go_id","ensembl_gene_id")],
+     TERM2NAME = go.all[ ,c("go_id", "name_1006")]
+ )
> 
> ## check
> as.data.frame(res.GO.ora)[1:15,]
                   ID                                  Description GeneRatio
GO:0000166 GO:0000166                           nucleotide binding    39/728
GO:0009693 GO:0009693                ethylene biosynthetic process     6/728
GO:0009414 GO:0009414                response to water deprivation    12/728
GO:0009651 GO:0009651                      response to salt stress    13/728
GO:0004674 GO:0004674     protein serine/threonine kinase activity    29/728
GO:0016740 GO:0016740                         transferase activity    37/728
GO:0008152 GO:0008152                            metabolic process    14/728
GO:0009835 GO:0009835                               fruit ripening     6/728
GO:0050896 GO:0050896                         response to stimulus    11/728
GO:0009060 GO:0009060                          aerobic respiration     8/728
GO:0009735 GO:0009735                        response to cytokinin     8/728
GO:0071281 GO:0071281                cellular response to iron ion     5/728
GO:0006817 GO:0006817                      phosphate ion transport     9/728
GO:0002238 GO:0002238        response to molecule of fungal origin     6/728
GO:0016798 GO:0016798 hydrolase activity, acting on glycosyl bonds    11/728
             BgRatio       pvalue     p.adjust       qvalue
GO:0000166 410/21730 5.405612e-09 5.405612e-09 3.260438e-06
GO:0009693  10/21730 2.593079e-07 2.593079e-07 7.820182e-05
GO:0009414  60/21730 5.843704e-07 5.843704e-07 1.174892e-04
GO:0009651  81/21730 2.769484e-06 2.769484e-06 3.391962e-04
GO:0004674 335/21730 3.346054e-06 3.346054e-06 3.391962e-04
GO:0016740 486/21730 3.374203e-06 3.374203e-06 3.391962e-04
GO:0008152  97/21730 4.233089e-06 4.233089e-06 3.647459e-04
GO:0009835  15/21730 5.351367e-06 5.351367e-06 4.034649e-04
GO:0050896  63/21730 6.963830e-06 6.963830e-06 4.666988e-04
GO:0009060  34/21730 1.280045e-05 1.280045e-05 7.720691e-04
GO:0009735  36/21730 2.010722e-05 2.010722e-05 1.102530e-03
GO:0071281  14/21730 6.478359e-05 6.478359e-05 3.256228e-03
GO:0006817  55/21730 8.090365e-05 8.090365e-05 3.753668e-03
GO:0002238  24/21730 1.111763e-04 1.111763e-04 4.789777e-03
GO:0016798  85/21730 1.238198e-04 1.238198e-04 4.843169e-03
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           geneID
GO:0000166 Solyc12g095850.2/Solyc06g073870.3/Solyc01g011093.1/Solyc11g006180.2/Solyc10g078560.2/Solyc07g062080.3/Solyc07g056140.3/Solyc08g008220.3/Solyc02g093300.3/Solyc07g005030.3/Solyc11g020040.2/Solyc02g084760.3/Solyc10g086410.3/Solyc12g010360.2/Solyc06g073330.3/Solyc05g043420.1/Solyc10g047140.2/Solyc05g056255.1/Solyc07g017540.3/Solyc07g049180.3/Solyc07g055640.1/Solyc09g009720.1/Solyc06g009970.3/Solyc07g055360.1/Solyc03g121780.1/Solyc04g072570.3/Solyc08g061220.3/Solyc12g044920.2/Solyc07g056580.3/Solyc04g081400.3/Solyc05g052270.2/Solyc03g031980.3/Solyc04g050850.2/Solyc01g102410.3/Solyc11g071870.2/Solyc02g070730.1/Solyc07g056350.3/Solyc02g064920.1/Solyc06g069230.3
GO:0009693                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Solyc07g049550.3/Solyc02g091990.3/Solyc09g089580.3/Solyc02g036350.3/Solyc02g081190.3/Solyc12g005940.2
GO:0009414                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Solyc04g082700.3/Solyc08g081190.3/Solyc02g062390.3/Solyc05g055990.3/Solyc01g107880.3/Solyc02g083510.3/Solyc04g078900.3/Solyc11g069430.2/Solyc09g075820.3/Solyc08g005610.3/Solyc12g006850.2/Solyc01g108280.3
GO:0009651                                                                                                                                                                                                                                                                                                                                                                                                                                                           Solyc12g015640.2/Solyc07g049550.3/Solyc01g098350.3/Solyc01g091650.3/Solyc06g008820.3/Solyc09g075820.3/Solyc12g006850.2/Solyc02g085730.3/Solyc02g036350.3/Solyc01g108280.3/Solyc05g018520.3/Solyc02g081190.3/Solyc12g005940.2
GO:0004674                                                                                                                                                                           Solyc06g053730.1/Solyc07g062080.3/Solyc03g025360.3/Solyc08g077990.3/Solyc05g052590.1/Solyc02g090980.1/Solyc10g085680.2/Solyc04g011520.3/Solyc01g088690.3/Solyc03g005130.2/Solyc01g099280.3/Solyc03g117550.1/Solyc04g078870.3/Solyc03g005330.1/Solyc02g079533.1/Solyc02g090990.1/Solyc07g049180.3/Solyc07g055640.1/Solyc07g040720.3/Solyc03g121780.1/Solyc01g010950.3/Solyc05g052270.2/Solyc03g031980.3/Solyc06g066130.1/Solyc02g087510.3/Solyc07g056350.3/Solyc01g108280.3/Solyc02g064920.1/Solyc07g005440.1
GO:0016740                                   Solyc11g006180.2/Solyc08g077080.1/Solyc06g007980.3/Solyc07g062080.3/Solyc07g056140.3/Solyc08g008220.3/Solyc02g093300.3/Solyc12g010600.2/Solyc02g084760.3/Solyc11g012240.1/Solyc12g006450.2/Solyc10g047140.2/Solyc12g009150.2/Solyc11g066270.2/Solyc07g049180.3/Solyc07g055640.1/Solyc09g009720.1/Solyc01g081050.3/Solyc07g056490.3/Solyc03g121780.1/Solyc08g075160.3/Solyc01g099630.3/Solyc04g072570.3/Solyc05g041320.1/Solyc07g056580.3/Solyc04g081400.3/Solyc05g052270.2/Solyc03g031980.3/Solyc08g068730.1/Solyc02g071040.3/Solyc02g091490.3/Solyc11g071870.2/Solyc07g056350.3/Solyc02g080570.3/Solyc02g064920.1/Solyc02g094635.1/Solyc11g006350.1
GO:0008152                                                                                                                                                                                                                                                                                                                                                                                                                                          Solyc08g082170.3/Solyc07g049370.2/Solyc02g082920.3/Solyc07g056140.3/Solyc11g066270.2/Solyc03g083910.3/Solyc04g015530.2/Solyc01g081050.3/Solyc08g075160.3/Solyc01g099630.3/Solyc01g059965.1/Solyc04g081440.3/Solyc09g075360.3/Solyc11g006350.1
GO:0009835                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Solyc07g049550.3/Solyc02g091990.3/Solyc09g089580.3/Solyc08g005610.3/Solyc07g064190.2/Solyc12g005940.2
GO:0050896                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Solyc04g082700.3/Solyc12g089180.2/Solyc04g076960.3/Solyc02g085170.3/Solyc03g032040.3/Solyc01g098500.3/Solyc12g099070.1/Solyc05g052270.2/Solyc09g075820.3/Solyc01g058360.1/Solyc05g053410.3
GO:0009060                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Solyc05g023920.1/Solyc07g053150.3/Solyc08g029280.1/Solyc04g055030.2/Solyc02g011800.1/Solyc01g065597.1/Solyc11g063610.2/Solyc02g011790.1
GO:0009735                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Solyc01g111170.3/Solyc07g049550.3/Solyc09g011810.3/Solyc11g045520.2/Solyc08g061260.3/Solyc02g036350.3/Solyc02g081190.3/Solyc12g005940.2
GO:0071281                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Solyc07g049550.3/Solyc11g045520.2/Solyc02g036350.3/Solyc02g081190.3/Solyc12g005940.2
GO:0006817                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Solyc04g082700.3/Solyc12g089180.2/Solyc04g076960.3/Solyc02g085170.3/Solyc03g032040.3/Solyc01g098500.3/Solyc12g099070.1/Solyc09g075820.3/Solyc01g058360.1
GO:0002238                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Solyc07g049550.3/Solyc07g056670.3/Solyc09g089580.3/Solyc02g036350.3/Solyc02g081190.3/Solyc12g005940.2
GO:0016798                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Solyc08g082170.3/Solyc07g049370.2/Solyc02g082920.3/Solyc11g066270.2/Solyc03g083910.3/Solyc04g015530.2/Solyc01g081050.3/Solyc01g099630.3/Solyc01g059965.1/Solyc04g081440.3/Solyc09g075360.3
           Count
GO:0000166    39
GO:0009693     6
GO:0009414    12
GO:0009651    13
GO:0004674    29
GO:0016740    37
GO:0008152    14
GO:0009835     6
GO:0050896    11
GO:0009060     8
GO:0009735     8
GO:0071281     5
GO:0006817     9
GO:0002238     6
GO:0016798    11
> 
> 
> ## limit analysis to only GO-BP categories
> res.GO.ora.bp <- enricher(
+     gene=genes.random,
+     pvalueCutoff = 1,
+     pAdjustMethod = "none",
+     universe=go.all$ensembl_gene_id,
+     minGSSize = 10,
+     maxGSSize = 500,
+     qvalueCutoff = 1,
+     TERM2GENE = go.all[go.all$namespace_1003 == "biological_process",  c("go_id","ensembl_gene_id")],
+     TERM2NAME = go.all[go.all$namespace_1003 == "biological_process",  c("go_id","name_1006")]
+ )
> 
> 
> ## check
> as.data.frame(res.GO.ora.bp)[1:15,]
                   ID                           Description GeneRatio  BgRatio
GO:0009693 GO:0009693         ethylene biosynthetic process     6/622 10/13877
GO:0009414 GO:0009414         response to water deprivation    12/622 60/13877
GO:0009835 GO:0009835                        fruit ripening     6/622 15/13877
GO:0009651 GO:0009651               response to salt stress    13/622 81/13877
GO:0050896 GO:0050896                  response to stimulus    11/622 63/13877
GO:0009060 GO:0009060                   aerobic respiration     8/622 34/13877
GO:0008152 GO:0008152                     metabolic process    14/622 97/13877
GO:0009735 GO:0009735                 response to cytokinin     8/622 36/13877
GO:0071281 GO:0071281         cellular response to iron ion     5/622 14/13877
GO:0002238 GO:0002238 response to molecule of fungal origin     6/622 24/13877
GO:0006817 GO:0006817               phosphate ion transport     9/622 55/13877
GO:0008645 GO:0008645        hexose transmembrane transport     6/622 28/13877
GO:0009805 GO:0009805         coumarin biosynthetic process     6/622 28/13877
GO:0006520 GO:0006520 cellular amino acid metabolic process     8/622 51/13877
GO:0006099 GO:0006099              tricarboxylic acid cycle     7/622 43/13877
                 pvalue     p.adjust       qvalue
GO:0009693 1.425001e-06 1.425001e-06 0.0004710002
GO:0009414 1.147147e-05 1.147147e-05 0.0018958106
GO:0009835 2.799818e-05 2.799818e-05 0.0030847118
GO:0009651 5.877688e-05 5.877688e-05 0.0048255850
GO:0050896 9.865574e-05 9.865574e-05 0.0048255850
GO:0009060 1.003814e-04 1.003814e-04 0.0048255850
GO:0008152 1.021979e-04 1.021979e-04 0.0048255850
GO:0009735 1.545599e-04 1.545599e-04 0.0063857647
GO:0071281 2.542504e-04 2.542504e-04 0.0093373828
GO:0002238 5.329441e-04 5.329441e-04 0.0176152062
GO:0006817 6.903351e-04 6.903351e-04 0.0207430826
GO:0008645 1.280490e-03 1.280490e-03 0.0325565838
GO:0009805 1.280490e-03 1.280490e-03 0.0325565838
GO:0006520 1.800752e-03 1.800752e-03 0.0425139979
GO:0006099 2.772708e-03 2.772708e-03 0.0576747680
                                                                                                                                                                                                                                                  geneID
GO:0009693                                                                                                                                         Solyc07g049550.3/Solyc02g091990.3/Solyc09g089580.3/Solyc02g036350.3/Solyc02g081190.3/Solyc12g005940.2
GO:0009414                                   Solyc04g082700.3/Solyc08g081190.3/Solyc02g062390.3/Solyc05g055990.3/Solyc01g107880.3/Solyc02g083510.3/Solyc04g078900.3/Solyc11g069430.2/Solyc09g075820.3/Solyc08g005610.3/Solyc12g006850.2/Solyc01g108280.3
GO:0009835                                                                                                                                         Solyc07g049550.3/Solyc02g091990.3/Solyc09g089580.3/Solyc08g005610.3/Solyc07g064190.2/Solyc12g005940.2
GO:0009651                  Solyc12g015640.2/Solyc07g049550.3/Solyc01g098350.3/Solyc01g091650.3/Solyc06g008820.3/Solyc09g075820.3/Solyc12g006850.2/Solyc02g085730.3/Solyc02g036350.3/Solyc01g108280.3/Solyc05g018520.3/Solyc02g081190.3/Solyc12g005940.2
GO:0050896                                                    Solyc04g082700.3/Solyc12g089180.2/Solyc04g076960.3/Solyc02g085170.3/Solyc03g032040.3/Solyc01g098500.3/Solyc12g099070.1/Solyc05g052270.2/Solyc09g075820.3/Solyc01g058360.1/Solyc05g053410.3
GO:0009060                                                                                                       Solyc05g023920.1/Solyc07g053150.3/Solyc08g029280.1/Solyc04g055030.2/Solyc02g011800.1/Solyc01g065597.1/Solyc11g063610.2/Solyc02g011790.1
GO:0008152 Solyc08g082170.3/Solyc07g049370.2/Solyc02g082920.3/Solyc07g056140.3/Solyc11g066270.2/Solyc03g083910.3/Solyc04g015530.2/Solyc01g081050.3/Solyc08g075160.3/Solyc01g099630.3/Solyc01g059965.1/Solyc04g081440.3/Solyc09g075360.3/Solyc11g006350.1
GO:0009735                                                                                                       Solyc01g111170.3/Solyc07g049550.3/Solyc09g011810.3/Solyc11g045520.2/Solyc08g061260.3/Solyc02g036350.3/Solyc02g081190.3/Solyc12g005940.2
GO:0071281                                                                                                                                                          Solyc07g049550.3/Solyc11g045520.2/Solyc02g036350.3/Solyc02g081190.3/Solyc12g005940.2
GO:0002238                                                                                                                                         Solyc07g049550.3/Solyc07g056670.3/Solyc09g089580.3/Solyc02g036350.3/Solyc02g081190.3/Solyc12g005940.2
GO:0006817                                                                                      Solyc04g082700.3/Solyc12g089180.2/Solyc04g076960.3/Solyc02g085170.3/Solyc03g032040.3/Solyc01g098500.3/Solyc12g099070.1/Solyc09g075820.3/Solyc01g058360.1
GO:0008645                                                                                                                                         Solyc04g082700.3/Solyc12g089180.2/Solyc02g085170.3/Solyc03g032040.3/Solyc12g099070.1/Solyc09g075820.3
GO:0009805                                                                                                                                         Solyc07g049550.3/Solyc07g056670.3/Solyc09g089580.3/Solyc02g036350.3/Solyc02g081190.3/Solyc12g005940.2
GO:0006520                                                                                                       Solyc10g078560.2/Solyc12g014100.2/Solyc09g064430.3/Solyc03g045020.3/Solyc02g091990.3/Solyc02g063540.2/Solyc03g120090.1/Solyc11g006350.1
GO:0006099                                                                                                                        Solyc07g055840.3/Solyc09g015495.1/Solyc06g009820.3/Solyc04g055030.2/Solyc01g005560.3/Solyc07g062530.3/Solyc11g007990.2
           Count
GO:0009693     6
GO:0009414    12
GO:0009835     6
GO:0009651    13
GO:0050896    11
GO:0009060     8
GO:0008152    14
GO:0009735     8
GO:0071281     5
GO:0002238     6
GO:0006817     9
GO:0008645     6
GO:0009805     6
GO:0006520     8
GO:0006099     7
> 
> 
> 
> ## PART 5: generate some plots to visualize results
> library(enrichplot)
> 
> barplot(res.GO.ora.bp, showCategory=10)
> dotplot(res.GO.ora.bp, showCategory=10)
> cnetplot(res.GO.ora.bp, showCategory=10)
> heatplot(res.GO.ora.bp, showCategory=10)
> 
> layout.params = list(layout = "kk")
> cex.params = list(category_node = 1.5)
> emapplot( pairwise_termsim(res.GO.ora.bp),
+           cex.params=cex.params,
+           layout.params=layout.params)
> 
> 

> sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: Europe/Amsterdam
tzcode source: internal

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

other attached packages:
[1] enrichplot_1.20.0     clusterProfiler_4.8.1 biomaRt_2.56.1       

loaded via a namespace (and not attached):
  [1] DBI_1.1.3               bitops_1.0-7            gson_0.1.0              shadowtext_0.1.2       
  [5] gridExtra_2.3           rlang_1.1.1             magrittr_2.0.3          DOSE_3.26.1            
  [9] compiler_4.3.0          RSQLite_2.3.1           png_0.1-8               vctrs_0.6.3            
 [13] reshape2_1.4.4          stringr_1.5.0           pkgconfig_2.0.3         crayon_1.5.2           
 [17] fastmap_1.1.1           dbplyr_2.3.2            XVector_0.40.0          labeling_0.4.2         
 [21] ggraph_2.1.0            utf8_1.2.3              HDO.db_0.99.1           purrr_1.0.1            
 [25] bit_4.0.5               zlibbioc_1.46.0         cachem_1.0.8            aplot_0.1.10           
 [29] GenomeInfoDb_1.36.0     jsonlite_1.8.5          progress_1.2.2          blob_1.2.4             
 [33] BiocParallel_1.34.2     tweenr_2.0.2            prettyunits_1.1.1       parallel_4.3.0         
 [37] R6_2.5.1                stringi_1.7.12          RColorBrewer_1.1-3      GOSemSim_2.26.0        
 [41] Rcpp_1.0.10             downloader_0.4          IRanges_2.34.0          Matrix_1.5-4.1         
 [45] splines_4.3.0           igraph_1.5.0            tidyselect_1.2.0        qvalue_2.32.0          
 [49] viridis_0.6.3           codetools_0.2-19        curl_5.0.1              lattice_0.21-8         
 [53] tibble_3.2.1            plyr_1.8.8              Biobase_2.60.0          treeio_1.24.1          
 [57] withr_2.5.0             KEGGREST_1.40.0         gridGraphics_0.5-1      BiocFileCache_2.8.0    
 [61] scatterpie_0.2.1        polyclip_1.10-4         xml2_1.3.4              Biostrings_2.68.1      
 [65] filelock_1.0.2          pillar_1.9.0            ggtree_3.8.0            stats4_4.3.0           
 [69] ggfun_0.0.9             generics_0.1.3          RCurl_1.98-1.12         hms_1.1.3              
 [73] S4Vectors_0.38.1        ggplot2_3.4.2           munsell_0.5.0           scales_1.2.1           
 [77] tidytree_0.4.2          glue_1.6.2              lazyeval_0.2.2          tools_4.3.0            
 [81] ggnewscale_0.4.9        data.table_1.14.8       fgsea_1.26.0            XML_3.99-0.14          
 [85] graphlayouts_1.0.0      fastmatch_1.1-3         tidygraph_1.2.3         cowplot_1.1.1          
 [89] grid_4.3.0              tidyr_1.3.0             ape_5.7-1               AnnotationDbi_1.62.1   
 [93] colorspace_2.1-0        nlme_3.1-162            GenomeInfoDbData_1.2.10 patchwork_1.1.2        
 [97] ggforce_0.4.1           cli_3.6.1               rappdirs_0.3.3          fansi_1.0.4            
[101] viridisLite_0.4.2       dplyr_1.1.2             gtable_0.3.3            yulab.utils_0.0.6      
[105] digest_0.6.31           BiocGenerics_0.46.0     ggrepel_0.9.3           ggplotify_0.1.0        
[109] farver_2.1.1            memoise_2.0.1           lifecycle_1.0.3         httr_1.4.6             
[113] GO.db_3.17.0            bit64_4.0.5             MASS_7.3-60            
>