User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu2.0k
Reputation:
1,960
Status:
Trusted
Location:
China/Hong Kong/The University of Hong Kong
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
3 days, 16 hours ago
Joined:
6 years, 11 months ago
Email:
g************@gmail.com

I study Systems Biology at The University of Hong Kong.

Email: guangchuangyu@gmail.com

Posts by Guangchuang Yu

<prev • 181 results • page 1 of 19 • next >
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Comment: C: Showing more terms in the result of GESA by ClusterProfiler
... pls also try different `qvalueCutoff`. ...
written 17 days ago by Guangchuang Yu2.0k
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Answer: A: extract gseaResult in clusterprofiler
... `as.data.frame` to convert the object to data frame? ...
written 19 days ago by Guangchuang Yu2.0k
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Comment: C: ClusterProfiler cannot map any gene
... see and the package vignette. You need to specify the ID type if it is supported. ...
written 25 days ago by Guangchuang Yu2.0k
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Comment: C: ClusterProfiler cannot map any gene
... no it does work with gene symbol if you specify the `keyType = "SYMBOL"` ...
written 25 days ago by Guangchuang Yu2.0k
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Answer: A: How to convert fasta file format to phylip file format
... `ggtree` support `phylip` tree format but not `phylip` mutiple sequence alignment. the `phylip` tree file contains msa in the famous `phylip` format with additional record of corresponding tree in `newick` text. `ggtree` supports visualizing phylogenetic tree and you need to have a tree before pas ...
written 5 weeks ago by Guangchuang Yu2.0k
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Answer: A: GSEA results change in clusterProfiler
... `as.data.frame` also works for `clusterProfiler`'s `GSEA` output. ...
written 5 weeks ago by Guangchuang Yu2.0k
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Comment: C: Difference between ape::root, ggtree::reroot and phytools::reroot in R
... currently `ggtree::reroot` call `phytools::reroot` by specifying the position at the middle of the edge. ...
written 9 weeks ago by Guangchuang Yu2.0k
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Comment: C: mgeneSim function in GOSemSim package: error: r in go_matrix[gos[[i]], gos[[j]]]
... in GOSemSim v>=2.6.1, `mgeneSim` will always output a matrix. ``` > similarity_matrix 3600 3600 0.189 ``` ...
written 9 weeks ago by Guangchuang Yu2.0k
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Comment: C: mgeneSim function in GOSemSim package: error: r in go_matrix[gos[[i]], gos[[j]]]
... By design, all the NA columns and rows will be removed. This is why the output is 1. As you only have 1 GO term and the similarity of a GO term to itself is always 1 using Wang's method. ...
written 10 weeks ago by Guangchuang Yu2.0k
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Answer: A: mgeneSim function in GOSemSim package: error: r in go_matrix[gos[[i]], gos[[j]]]
... ``` > clusterProfiler::bitr(an_Entrez_ID_vector, 'ENTREZID', 'GO', OrgDb='org.Hs.eg.db') 'select()' returned 1:many mapping between keys and columns ENTREZID GO EVIDENCE ONTOLOGY 1 9895 GO:0005515 IPI MF 2 9895 GO:0006914 IEA BP 4 54621 GO:0016021 ...
written 10 weeks ago by Guangchuang Yu2.0k

Latest awards to Guangchuang Yu

Scholar 4 weeks ago, created an answer that has been accepted. For A: R:Cannot install snpStats packages
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Appreciated 3 months ago, created a post with more than 5 votes. For ggtree: phylogenetic tree visualization and annotation
Popular Question 5 months ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Get All The Genes In A Pathway (E.G. Kegg)
Scholar 8 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Popular Question 10 months ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
Popular Question 14 months ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Scholar 15 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Appreciated 17 months ago, created a post with more than 5 votes. For A: specific string extraction use excel, R or Python
Popular Question 18 months ago, created a question with more than 1,000 views. For clusterProfiler: an R package for comparing biological themes among gene clusters
Popular Question 20 months ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Scholar 21 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
Scholar 22 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
Centurion 2.0 years ago, created 100 posts.
Scholar 2.0 years ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Guru 2.0 years ago, received more than 100 upvotes.

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