User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.9k
Reputation:
1,890
Status:
Trusted
Location:
China/Hong Kong/The University of Hong Kong
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
4 days, 12 hours ago
Joined:
6 years, 9 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 • 175 results • page 1 of 18 • next >
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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 10 days ago by Guangchuang Yu1.9k
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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 12 days ago by Guangchuang Yu1.9k
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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 14 days ago by Guangchuang Yu1.9k
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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 17 days ago by Guangchuang Yu1.9k
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Answer: A: Downstream proportions are not identical in vennpie and upsetplot results
... thanks for reporting this issue. It has been fixed in `v=1.16.1`. ...
written 4 weeks ago by Guangchuang Yu1.9k
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Answer: A: upsetplot in clusterprofiler
... `upsetplot` is indeed supported, see . ...
written 4 weeks ago by Guangchuang Yu1.9k
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Comment: A: Downstream proportions are not identical in vennpie and upsetplot results
... any reproducible example? ...
written 5 weeks ago by Guangchuang Yu1.9k
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Answer: A: How to get the all the overlap information of a peak in ChIPseeker
... `peakAnno@detailGenomicAnnotation` ...
written 5 weeks ago by Guangchuang Yu1.9k
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Answer: A: how does ggtree interprets branch support value (e.g bootstrap value) given as n
... This is an issue of re-root, you should ask the author of `ape` for the `ape::root` function. ...
written 6 weeks ago by Guangchuang Yu1.9k • updated 6 weeks ago by zx87544.8k
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Answer: A: Enrichpathway In ReactomePA.
... ``` > yy # # over-representation test # #...@organism human #...@ontology Reactome #...@keytype ENTREZID #...@gene chr [1:198] "64240" "6296" "196883" "153" "155" "4299" "2334" "79026" ... #...pvalues adjusted by 'BH' with cutoff <1 #...441 enriched terms found 'data.frame': 441 obs. o ...
written 4 months ago by Guangchuang Yu1.9k

Latest awards to Guangchuang Yu

Appreciated 6 weeks ago, created a post with more than 5 votes. For ggtree: phylogenetic tree visualization and annotation
Popular Question 3 months ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: GO Enrichment Analysis representation
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Get All The Genes In A Pathway (E.G. Kegg)
Scholar 6 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Popular Question 8 months ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
Popular Question 13 months ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Scholar 13 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Appreciated 15 months ago, created a post with more than 5 votes. For A: specific string extraction use excel, R or Python
Popular Question 17 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 18 months ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Scholar 19 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
Scholar 20 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
Teacher 21 months ago, created an answer with at least 3 up-votes. 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
Centurion 22 months ago, created 100 posts.
Scholar 22 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Guru 22 months ago, received more than 100 upvotes.
Scholar 23 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Supporter 23 months ago, voted at least 25 times.

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