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#1pairwise_termsim in GuangchuangYu/enrichplot - RDRR.io
This function add similarity matrix to the termsim slot of enrichment result. Users can use the 'method' parameter to select the method of ...
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#2enrichplot/pairwise_termsim.R at master - GitHub
@exportMethod pairwise_termsim. setMethod("pairwise_termsim", signature(x = "enrichResult"),. function(x, method = "JC", semData = NULL, showCategory = 200) ...
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#3enrichplot: Visualization of Functional ... - Bioconductor
terms is obtained by function 'pairwise_termsim', the details of similarity calculation can be found in its documentation: pairwise_termsim.
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#4Chapter 15 Visualization of functional enrichment result
It relies on the pairwise similarities of the enriched terms calculated by the pairwise_termsim() function, which by default using Jaccard's similarity ...
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#5emapplot-原来能用的函数，现在报错了肿么办 - 简书
Please use pairwise_termsim function to deal with the results of enrichment analysis. 经过核实，我问了他的版本是1.10.0，我的版本是1.4.0， ...
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#6Functional Analysis for RNA-seq - GitHub Pages
Before creating the plot, we will need to obtain the similarity between terms using the pairwise_termsim() function (instructions for emapplot).
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#7GO、KEGG富集分析与enrichplot超全可视化攻略 - 知乎专栏
treeplot对富集结果术语进行层次聚类, 并使用高频词标记，有助于我们从繁多的富集结果中快速提取有用关键信息。 使用treeplot也需要用pairwise_termsim()处理富集结果。 ## ...
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#8enrichplot – R documentation - Quantargo
pairwise_termsim. pairwise_termsim · plotting.clusterProfile. plotting-clusterProfile · pmcplot. pmcplot · reexports. Objects exported from other packages.
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#9Treeplot - BioStars
Here is my code chunk. library(enrichplot). edox2 <- pairwise_termsim(ego3). treeplot(edox2, hclust_method = "average", label_format = 30).
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#10enrichplot: Visualization of Functional ... - Bioconductor
xx2 <- pairwise_termsim(xx) cnetplot(xx2). ## End(Not run) color_palette color_palette. Description create color palette for continuous data.
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#11让你的基因有名字 - 腾讯云- Tencent
Please use pairwise_termsim function to deal with the result. 处理方法：. library(enrichplot) ego_CC2 <- pairwise_termsim(ego_CC) ...
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#12enrichplot package - RDocumentation
Objects exported from other packages. ridgeplot. ridgeplot. gseadist. gseadist. gseaplot. gseaplot. pairwise_termsim. pairwise_termsim. treeplot. treeplot.
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#13Customizing graph parameters not explicitly listed as function ...
Hs.eg.db', 'ENTREZID') edox2 <- enrichplot::pairwise_termsim(edox) p1 <- treeplot(edox2) p1. Link to example graph on the left, ...
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#14Stronger transcriptomic response to feed intake in ... - bioRxiv
and simplified enriched ontologies were clustered using the pairwise_termsim() function. The upset plot was generated using the {UpSetR} ...
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#15Enrichment analysis - RPubs
x2 = pairwise_termsim(gse) emapplot(x2, showCategory = 20). Enrichment map organizes enriched terms into a network with edges connecting ...
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#16Package 'enrichplot' - TU Dortmund
Value a igraph object. Author(s). Guangchuang Yu pairwise_termsim pairwise_termsim. Description. Get the similarity matrix. Usage.
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#17差异表达基因富集结果可视化原创 - CSDN博客
res1 <- enrichplot::pairwise_termsim(res1). # pairwise_termsim {enrichplot}:Get the similarity matrix. emapplot(res1, showCategory = 15, ...
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#18Integrated analyses of the methylome and transcriptome to ...
For GO terms, the function pairwise_termsim () from enrichplot was used to calculate the Jaccard correlation coefficient among terms, ...
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#19让你的基因有名字 - 生信菜鸟团
Please use pairwise_termsim function to deal with the result. 处理方法： library(enrichplot) ego_CC2 <- pairwise_termsim(ego_CC) ...
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#20【R】Rを用いたエンリッチメント解析のやり方 ... - LabCode
pairwise_termsim 関数は、共通のアノテーション項目を持つ2つ以上のリストを取り、そのアノテーション項目の共通性に基づいて、各リストのすべてのペアの ...
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#21R]单细胞之富集分析- mdnice 墨滴
emapplot(pairwise_termsim(go.results)). “gene_convert <- bitr(markers$gene, fromType = 'SYMBOL', toType = 'ENTREZID', OrgDb = OrgDb)”作用：.
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#22clusterProfiler 4.0: A universal enrichment tool for interpreting ...
ego <- pairwise_termsim(ego) ego2 <- pairwise_termsim(ego2) p1 <- emapplot(ego, cex_label_category=.8, cex_line=.5) + coord_cartesian().
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#2301_diffAnalysis.R · master · GenEpi / Analyses / rosePigs
egosimpl <- map(egosimpl, pairwise_termsim). 399. 400. map_int(egosimpl, \(x) nrow(x@result)). 401. # PvsM_all PvsM_upr PvsM_dow FvsFinP_all ...
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#24Rhistory · master · Eugenie Lohmann / LIVER_on_metabolic
... maxGSSize=Inf) edo_go[['liver']] <- pairwise_termsim(GSEA_go[['liver']]) edo_go[['pancreas']] <- pairwise_termsim(GSEA_go[['pancreas']]) ...
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#251. Required packages 2. Data processing and visualization in ...
pairwise_termsim (gsea_kegg) %>% emapplot(layout="kk"). Page 43. ridge plot ridgeplot(gsea_kegg) + labs(x = 'NES', title= 'ridge plot for GSEA') +.
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#26富集分析—— clusterProfiler：Visualization - JOYK
它依赖于pairwise_termsim()函数计算的丰富项的成对相似性，默认情况下使用Jaccard 的相似性指数(JC)。如果支持，用户还可以使用语义相似度值（例如，GO、DO和MeSH）。
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#27Bioconductor Install [XERLR7]
Pairwise_termsim : pairwise_termsim in GuangchuangYu . Fasta , which works fine, except for one crucial point: there's supposed to be a maximum number of ...
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#28基因富集分析- 静风-fish - 博客园
... width = 9, height = 7) x2 <- pairwise_termsim(kk) emapplot(x2, showCategory = 20, cex_label_category=0.65, color="pvalue", ...
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#29Lemna minor annotation R package (org.Lminor.eg.db) and ...
Lminor.eg.db', ont="BP", computeIC=FALSE, keytype = "GID") res = enrichplot::pairwise_termsim(res, method = "Wang", semData = d) # Rmv GO ...
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#30Intergenerational impact of dietary protein restriction in dairy ...
The function pairwise_termsim() from enrichplot was used to calculate the Jaccard correlation coefficient among GO terms.
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#31Assessing the quality of comparative genomics data and ...
on semantic similarities calculated with the function pairwise_termsim() from the enrichplot package. .CC-BY 4.0 International licensemade ...
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#32Gene co-expression in response to Staphylococcus aureus ...
In addition, the pairwise similarities of enriched GO terms were calculated using “pairwise_termsim” function, and hierarchical clustering ...
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#33cell analysis reveals dynamics of human B cell differentiation ...
GSEA results was performed using the pairwise_termsim function from enrichplot with an adjusted p- value<0.05 and then plotted using the ...
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#34关于富集分析这件事，我有话想说… - 北美生活引擎
edox2 <- pairwise_termsim(edox)#这一步骤可以简单理解计算了GO结果之间彼此的相似度，其实就是在我们的富集结果中添加了这个信息，然后我们才可以 ...
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#35Enrichment analysis - Amazon AWS
x2 = pairwise_termsim(gse) emapplot(x2, showCategory = 20). Enrichment map organizes enriched terms into a network with edges connecting ...
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#36Enrichment 3 1 Answers - Bea Krebs
... package: enrichplot::emapplot(enrichplot::pairwise_termsim(AC_MAC_GO),. Bridge the Knowledge Gap taking the help of the Go Math Grade 1 Solution Key.
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#37Bioconductor Install (YD3TJZ)
Pairwise_termsim : pairwise_termsim in GuangchuangYu. The Comprehensive R Archive Network. Installing R packages from CRAN / Bioconductor / Omegahat / Github ...
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#38Bioconductor Install 7IJZS0
Pairwise_termsim : pairwise_termsim in GuangchuangYu. Install R: After adding the repository above, I install the following packages using either the command ...
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#39Bioconductor Install (UITP6G)
Pairwise_termsim : pairwise_termsim in GuangchuangYu. Pairwise_termsim: pairwise_termsim in GuangchuangYu . "Exome-based analysis for RNA epigenome ...
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#40Bioconductor Install (88BS2L)
Pairwise_termsim : pairwise_termsim in GuangchuangYu . Obviously, the handbrake is one of the most safety-crucial parts on the entire vehicle, ...
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