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#1Error in enrichGO function using keyType="SYMBOL" #222
I used the enrichGO funtion with the keyType="SYMBOL" option for a long time without any problem, but this time I get an error and it is ...
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#2keytype not supported in clusterprofiler when it is ensembl IDs?
ego <- enrichGO(gene = siggenes_set1, OrgDb = Mm,universe = allDEgenes, keyType="ENSEMBL",ont = "BP", pAdjustMethod = "BH", qvalueCutoff = 0.05, ...
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#3enrichGO function - RDocumentation
Given a vector of genes, this function will return the enrichment GO categories after FDR control. Usage. enrichGO(gene, OrgDb, keytype = "ENTREZID", ont = "MF" ...
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#4Chapter 6 GO enrichment analysis - YuLab@SMU
6.1 Supported organisms GO analyses (groupGO(), enrichGO() and... ... Users need to specify the keyType parameter to specify the input gene ID type.
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#5GO analysis using clusterProfiler - Guangchuang Yu
In github version of clusterProfiler, enrichGO and gseGO functions ... Hs.eg.db, keytype="ENTREZID") head(summary(egmt)) ## ID Description ...
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#6enrichGO: GO Enrichment Analysis of a gene set. Given a ...
gene. a vector of entrez gene id. OrgDb. OrgDb. keyType. keytype of input gene. ont. One of "BP", "MF", and "CC" subontologies, or "ALL" for all three.
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#7unable to find an inherited method for function 'keytypes' for ...
However, I have a error in the enrichGO(): Error in (function (classes, ... enrichGO( demo, OrgDb = CalbicansEntrez, keyType = "ENTREZID",
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#8Package 'clusterProfiler' - Bioconductor
enrichGO. GO Enrichment Analysis of a gene set. Given a vector of genes, this ... keyType one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'.
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#9统计| 结合clusterProfiler理解GO富集分析 - 简书
OrgDb库enrichGO默认gene type是entrezID，但其他OrgDb支持的类型（ENSEMBLE，SYMBOL等）都可以通过参数keyType指定。 ge...
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#10Statistical analysis and visualization of functional profiles for ...
... can be used in groupGO , enrichGO and gseGO by specifying keytype parameter. ... ego <- enrichGO(gene = gene, universe = names(geneList), OrgDb = org.
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#11GO enrichment - RPubs
Hs.eg.db) # convert EntrezID to gene symbol ego_ORA_90cutoff <- enrichGO(gene = gene_PC, OrgDb = org.Hs.eg.db, keyType = 'ENTREZID', ...
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#12使用clusterProfiler包利用eggnogmapper软件注释结果做GO和 ...
最开始的思路是先构建OrgDb，然后使用enrichGO和enrichKEGG函数做分析。但是最后遇到报错 Error in get_GO_data(OrgDb, ont, keyType) : keytype is not supported.
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#13Mapping nothing when doing Enrichment Analysis of the TAIR ...
ego <- enrichGO(syn_block1_gene, OrgDb = "org.At.tair.db", keyType = "TAIR",ont = "BP") > ego # # over-representation test # #.
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#14enrichGO function - YuLab-SMU/ClusterProfiler - Issue Explorer
ego_all <- enrichGO(gene = gene,keyType="GID", OrgDb = org.AnigerN402.eg.db,ont = "ALL",pAdjustMethod = "BH",qvalueCutoff = 0.05) Error in ...
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#15[annotation] clusterProfiler包- bioconductor中文 - 生信技能树
1）enrichGO：（GO富集分析）描述：GO Enrichment Analysis of a gene set. ... enrichGO(gene, OrgDb, keyType = "ENTREZID", ...
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#16Over-Representation Analysis with ClusterProfiler
keyType This is the source of the annotation (gene ids). ... go_enrich <- enrichGO(gene = genes, universe = names(gene_list), OrgDb = organism, keyType ...
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#17GEO数据挖掘小尝试：（三）利用clusterProfiler进行富集分析 ...
enrichGO GO Enrichment Analysis of a gene set. ... Usage: enrichGO(gene, OrgDb, keyType = "ENTREZID", ont = "MF", pvalueCutoff = 0.05, ...
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#18Enrichment Analysis by using clusterProlifer - 知乎专栏
BP = enrichGO(gene = DEG.entrez_id,. OrgDb = org.Hs.eg.db,. keyType = "ENTREZID",. ont = "BP",. pvalueCutoff = 0.05,. qvalueCutoff = 0.5).
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#19转录组入门——8 | blog - mysql学习记录
ego <- enrichGO(gene = diff_gene_ENSEMBL, OrgDb = org.Mm.eg.db, keytype = "ENSEMBL", ont = "BP", pAdjustMethod = "BH",
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#20clusterprofiler包进行GO与KEGG富集分析_twistti的博客
Hs.eg.db) #### GO: Over-Representation Analysis #### # Biological Process ego_BP <- enrichGO(gene = gene, keyType ='ENTREZID' , ont="BP", OrgDb = org.
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#21clusterProfiler：富集分析和可视化的强大工具 - 王进的个人网站
ego <- enrichGO( gene = gene, keyType = "ENTREZID", OrgDb = org.Hs.eg.db, ont = "CC", pAdjustMethod = "BH", pvalueCutoff = 0.01, ...
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#22使用clusterProfiler进行GO富集分析- 云+社区 - 腾讯云
ego <- enrichGO( gene = gene, keyType = "ENTREZID", OrgDb = org. ... gene 就是差异基因对应的向量， keyType 指定基因ID的类型，默认为 ENTREZID ...
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#23Exercise 2. Functional annotation of ChIP-peaks - CBSU
ego_MF <- enrichGO(gene =inform$geneId,'org.At.tair.db',keytype="TAIR",ont = "MF",pAdjustMethod = "BH",pvalueCutoff = 0.01,qvalueCutoff = 0.05).
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#24R语言enrichGo - CSDN
csdn已为您找到关于R语言enrichGo相关内容，包含R语言enrichGo相关文档代码介绍、 ... keytype = 'SYMBOL') #GO分析enrich_go <- enrichGO(gene=gene, OrgDb = 'org.
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#25Functional Analysis - STEM-Away
enrichGO (): performs enrichment analysis on a gene set to classify genes into different categories and bins ... keyType = 'ENTREZID').
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#26使用clusterProfiler進行GO富集分析 - 台部落
ego <- enrichGO( gene = gene, keyType = "ENTREZID", OrgDb = org.Hs.eg.db, ont = "CC", pAdjustMethod = "BH", pvalueCutoff = 0.01, ...
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#27富集分析一網打進 - GetIt01
readable=T: 原文檔無這個參數，使用的是setReadble函數nMF <- enrichGO(entrezID, "org.Hs.eg.db", ont = "MF", keytype = "ENTREZID",n pAdjustMethod = "BH", ...
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#28162-一个看似简单的需求——修改富集分析的dotplot图
先得到上调的差异基因gs_up，可以先不进行pvalue、qvalue的过滤 up <- enrichGO(gene = gs_up, keyType = 'ENSEMBL', OrgDb = org.
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#29RNASEQ20_Day3_Rscript.R
... signif_genes <- as.character(rownames(signif_res)) # Run GO enrichment analysis ego <- enrichGO(gene = signif_genes, universe = all_genes, keyType ...
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#30GO、GSEA富集分析一网打进-陈同的博文 - 科学
开始富集分析 # readable=T: 原文档无这个参数，使用的是setReadble函数MF <- enrichGO(entrezID, "org.Hs.eg.db", ont = "MF", keytype = "ENTREZID" ...
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#31Data Integration and Clustering Analysis of Glioblastoma ...
toType = c("ENSEMBL", "ENTREZID", 'GO'),. OrgDb = org.Hs.eg.db) rnaseq.meta.genes.ego <- enrichGO( gene. = rnaseq.meta.genes.df$ENSEMBL,. keyType.
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#32Gene Ontology analysis for DEGs of Arabidopsis | FL的生信笔记
At.tair.db) ## 看该数据库支持哪些基因名称类型，例如拟南芥支持AT1G01110 就是keytype="TAIR" ego <- enrichGO(gene = b, keyType = "TAIR", ...
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#33GO，KEGG，DO 富集分析 - 码农家园
enrich.go.bp = enrichGO(gene = DEG.entrez_id, OrgDb = org.Hs.eg.db, keyType = "ENTREZID", ont = "BP", pvalueCutoff = 0.01,
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#34Chapter 14 DEG GO Enrichment | Single Cell Multi-Omics ...
geneid.ls <- deg.ls %>% map(~{ # here for macaque gene.df <- select(org.Mmu.eg.db, keys = .x, columns = c("ENTREZID", "SYMBOL"), keytype = "SYMBOL") gene ...
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#35富集分析一網打進 - ITW01
readable=T: 原文件無這個引數，使用的是setReadble函式MF <- enrichGO(entrezID, "org.Hs.eg.db", ont = "MF", keytype = "ENTREZID", ...
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#36ggplot2绘制GO富集分析柱状图 - 博客园
Hs.eg.db) GO<-enrichGO(gene=gene_id,OrgDb = "org.Hs.eg.db",keyType = "ENSEMBL",ont="ALL",qvalueCutoff = 0.05,readable = T) #gene就是差异基因 ...
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#37使用clusterProfiler包利用eggnog-mapper軟體注釋結果做GO和 ...
最開始的思路是先構建OrgDb，然後使用enrichGO和enrichKEGG函數做分析。但是最後遇到報錯 Error in get_GO_data(OrgDb, ont, keyType) : keytype is ...
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#38master · Hannes Reinwald / thyroid paper - GitLab
Dr.eg.db, keys=row.names(x), keytype="ENSEMBL", column= colInfo, multiVals= "first") x[,paste0(colInfo)] <- anno x } t3 <- AnnoFun(t3, ...
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#39clusterProfiler包 - 术之多
enrichGO (gene, OrgDb, keyType = "ENTREZID", ont = "MF",pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2,
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#40使用clusterProfiler对非模式生物进行富集分析 - Xgenes
BP <- enrichGO(gene=data, OrgDb = Thecacao.OrgDb, keyType = “SYMBOL”,ont = “BP”,pvalueCutoff = 0.01,qvalueCutoff = 0.05,readable = T)
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#41clusterProfiler - gitmemory
Function "enrichGO()" output a null object, function "gseGO()" output gseaResult contains no gene ratio. Hi, the team of "clusterProfiler". I'm new to ...
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#42GGPLOT2 Draw GO Enrichment Analysis Column
Use ClusterProfiler's EnrichGO function to get GO analysis ... to the differential gene, the keytype specifies the type of gene ID, the default is entrezid, ...
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#43转录组入门（8）：富集分析
enrichGO (gene, OrgDb, keytype = "ENTREZID", ont = "MF",; pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2,; minGSSize = 10, ...
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#44Bioconductor clusterProfiler Package Sample Use Case
... for the enrichGO function. Since our genesOfInterest object uses the Ensembl geneID format, the appropriate keyType should be "ENSEMBL" ...
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#45(偽）從零開始學轉錄組（8）：富集分析_生信技能樹- 微文庫
enrichGO (gene, OrgDb, keytype = "ENTREZID", ont = "MF", ... keyType: 基因的命名方式， “kegg”, 'ncbi-geneid', 'ncib-proteinid' and 'uniprot' ...
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#46clusterProfiler富集分析 - 学术咖
... entrezID <- entrezID$V1 BP <- enrichGO(entrezID,"org. ... Mm.eg.db, keyType = "ENTREZID")#将KEGG结果ENTREZID转换成gene symble barplot(BP ...
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#47Clusterprofiler object 'GO2ONT' not found - Breathing Labs
enrichGO (gene=my_gene_ids, keyType = "FLYBASE", OrgDb = org.Dm.eg.db, ont="ALL", pAdjustMethod = "BH", qvalueCutoff = 0.05, readable = TRUE) ...
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#48GO和KEGG富集教程_种星星种月亮的博客-程序员资料
GO的富集分析. ALL <- enrichGO(gene_name, "org.Hs.eg.db", keyType = "ENTREZID",ont = 'ALL',pvalueCutoff = 0.05,pAdjustMethod = "BH", qvalueCutoff = 0.1, ...
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#49GO、GSEA富集分析一网打进
readable=T: 原文档无这个参数，使用的是setReadble函数. MF <- enrichGO(entrezID, "org.Hs.eg.db", ont = "MF", keytype = "ENTREZID",
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#50GO分析学习笔记 - RVDSD的个人笔记本
使用clusterProfiler这个包进行GO分析时，通常并不需要转换ID，所有的ID类型都可以由 OrgDb 文件提供，并且通过 keyType 参数在 groupGO ， enrichGO 和 ...
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#51failed to Biological Id Translator - General - RStudio Community
ego_MF <- enrichGO(gene = data.df$ENTREZID, universe = names(geneList),OrgDb ... enrichGO(gene, OrgDb, keyType = "ENTREZID", ont = "MF",
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#52Package clusterprofiler - PDF Free Download - DocPlayer.net
10 10 enrichgo A enrichresult instance enrichgo GO Enrichment Analysis of a ... GO categories after FDR control. enrichgo(gene, OrgDb, keytype = "ENTREZID", ...
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#53单细胞转录组基础分析七:差异基因富集分析 - 快资讯
Hs.eg.db', + keyType = 'SYMBOL', + ont = "ALL", + pAdjustMethod = "BH", ... ego_CC <- enrichGO(gene = row.names(sig_dge.celltype), ...
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#54R包clusterProfiler比较不同dataset富集结果 - Excel技巧
... 0.05) #必须指定keytype，GO富集ego <- enrichGO(gene=gene,OrgDb='org.Hs.eg.db',keyType='SYMBOL',ont= "ALL",pAdjustMethod="BH",pvalueCutoff ...
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#55富集分析一网打进 - 天下
readable=T: 原文档无这个参数，使用的是setReadble函数 MF <- enrichGO(entrezID, "org.Hs.eg.db", ont = "MF", keytype = "ENTREZID", ...
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#56【技术贴】如何从数据库挖掘基因并筛选TagSNP（医学篇 ...
MF <- enrichGO(gene = DE_list, #差异基因vector keyType ="ENTREZID", OrgDb = org.Hs.eg.db, #对应的OrgDb ont = "MF", #GO 分类名称，CC BP MF
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#57"Bioconductor" recuerda una vez más que aquellos que ...
Primer uso clusterpofiler::enrichGO Cómo llamar el código del tío Y. enrichGO <- function (gene, OrgDb, keyType = "ENTREZID", ont = "MF", ...
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#58Differentially expressed genes
Perform GO enrichment analysis ; library(clusterProfiler) library(org.Mm.eg.db) enrichGO.CC <- enrichGO(genelist, OrgDb = org.Mm.eg.db, keyType = ...
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#59通路富集分析图怎么画 - 阿赐网
BP = enrichGO(gene =degs.list, OrgDb = org.Hs.eg.db, keyType = "SYMBOL", ont = "BP", pvalueCutoff = 0.5, qvalueCutoff = 0.5) ...
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#60GO_KEGG富集分析clusterProfiler - 大专栏
gene = select(org.Hs.eg.db, keys=ensids, columns=cols, keytype="ENTREZID") ... ego_CC <- enrichGO(gene = gene$ENTREZID, OrgDb= org.Hs.eg.db, ont = "CC", ...
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#61Go enrichment - Bomberos Rionegro
1 Supported organisms GO analyses ( groupGO (), enrichGO () and gseGO ... Usage enrichGO(gene, OrgDb, keyType = "ENTREZID To do this, we first rank the ...
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#62Golang Key.Type方法代码示例 - 纯净天空
Golang Key.Type方法代码示例，github.com/heems/bssim/Godeps/_workspace/src/github.com/jbenet/go-datastore.Key.Type用法.
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#63Enrichment analysis in one go - Programmer Sought
... and the setReadble function is used MF <- enrichGO(entrezID, "org.Hs.eg.db", ont = "MF", keytype = "ENTREZID", pAdjustMethod = "BH", pvalueCutoff = 0.05 ...
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#64enrichGO function #350 - githubmemory
> ego_all <- enrichGO(gene = gene,keyType="GID", OrgDb = org.AnigerN402.eg.db,ont = "ALL",pAdjustMethod = "BH",qvalueCutoff = 0.05) Error in testForValidKeytype ...
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enrichgo 在 大象中醫 Youtube 的最佳解答
enrichgo 在 大象中醫 Youtube 的最佳解答