User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu2.4k
Reputation:
2,410
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Trusted
Location:
China/Guangzhou/Southern Medical University
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
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Google Scholar Page
Last seen:
3 months, 1 week ago
Joined:
9 years, 4 months ago
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Professor of Bioinformatics at Southern Medical University.

Email: guangchuangyu@gmail.com

Posts by Guangchuang Yu

<prev • 193 results • page 1 of 20 • next >
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Answer: A: How do I add circles to the tips of a phylogenetic tree that have white fill and
... ``` ggtree(tree) + geom_tippoint(size=3, fill="white", color="black", shape=21) ``` ...
written 3 months ago by Guangchuang Yu2.4k
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Answer: A: plotting trees in R: node labels from nexus tree files
... The `read.beast()` function in the [treeio](https://www.bioconductor.org/packages/treeio) package should be able to parse the file and then you can use the [ggtree](https://www.bioconductor.org/packages/ggtree) package to visualize the tree with or without associated data (e.g. posterior values). ...
written 3 months ago by Guangchuang Yu2.4k
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Answer: A: showing specific GO pathways in the dotplot or cnetplot
... Sorry for late reply. This is actually supported, see . ...
written 4 months ago by Guangchuang Yu2.4k
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Answer: A: R ggtree adding metadata based on tree structure
... The first column should be node numbers or labels for ggtree to link your data to the tree. Please refer to our paper, . There are a number of examples in the supplemental file. ...
written 16 months ago by Guangchuang Yu2.4k
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Answer: A: clusterProfiler enrichGO gene size filter with minGSSize doesn't seem to work
... The `minGSSize` and `maxGSSize` are used to restrict gene set size not for your gene list. If we looking at the formula, , they apply to the `M`. ...
written 16 months ago by Guangchuang Yu2.4k
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Answer: A: How do I annotate a tree with boostrap scores and color code clades in ggtree?
... see an example in for integrating bootstrap value. For data integration, we have published a paper, https://academic.oup.com/mbe/article/35/12/3041/5142656, with lots of examples in the supplemental files. ...
written 19 months ago by Guangchuang Yu2.4k
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Comment: C: R color tree ggtree
... updated link, . ...
written 22 months ago by Guangchuang Yu2.4k
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Answer: A: clusterProfiler: cnetplot with interactive output
... it is indeed not available in the latest release as all the visualization methods were rewrote from scratch using ggplot2. However, if you want to use the old methods, you can use the [doseplot](https://github.com/GuangchuangYu/doseplot) package. ...
written 22 months ago by Guangchuang Yu2.4k
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Answer: A: ClusterProfiler fails to find GO terms
... ``` > genes<-c("ENSG00000198886","ENSG00000198888","ENSG00000198763","ENSG00000198840","ENSG00000212907","ENSG00000198786","ENSG00000198695","ENSG00000198727","ENSG00000198804","ENSG00000198712","ENSG00000198938","ENSG00000198899","ENSG00000228253") > > > ego<-enrichGO(genes, O ...
written 23 months ago by Guangchuang Yu2.4k
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Answer: A: R tidytree ggtree error
... you need to install Bioconductor 3.8. ...
written 2.1 years ago by Guangchuang Yu2.4k

Latest awards to Guangchuang Yu

Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: specific string extraction use excel, R or Python
Appreciated 4 months ago, created a post with more than 5 votes. For A: specific string extraction use excel, R or Python
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Scholar 15 months ago, created an answer that has been accepted. For A: R:Cannot install snpStats packages
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Scholar 16 months ago, created an answer that has been accepted. For A: R:Cannot install snpStats packages
Scholar 18 months ago, created an answer that has been accepted. For A: R:Cannot install snpStats packages
Scholar 19 months ago, created an answer that has been accepted. For A: R:Cannot install snpStats packages
Scholar 22 months ago, created an answer that has been accepted. For A: R:Cannot install snpStats packages
Scholar 23 months ago, created an answer that has been accepted. For A: R:Cannot install snpStats packages
Great Question 2.1 years ago, created a question with more than 5,000 views. For ggtree: phylogenetic tree visualization and annotation
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Scholar 2.4 years ago, created an answer that has been accepted. For A: How to filter genes in R
Scholar 2.4 years ago, created an answer that has been accepted. For A: R:Cannot install snpStats packages
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Scholar 2.5 years ago, created an answer that has been accepted. For A: R:Cannot install snpStats packages
Popular Question 2.6 years ago, created a question with more than 1,000 views. For DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
Appreciated 2.7 years ago, created a post with more than 5 votes. For ggtree: phylogenetic tree visualization and annotation
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Popular Question 2.8 years ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Get All The Genes In A Pathway (E.G. Kegg)
Scholar 3.1 years ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Popular Question 3.3 years ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation

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