User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.5k
Reputation:
1,510
Status:
Trusted
Location:
China/Hong Kong/The University of Hong Kong
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
1 day, 8 hours ago
Joined:
5 years, 8 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 • 148 results • page 1 of 15 • next >
2
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139
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Comment: C: Chip-seq peak annotation [Chipseeker]
... I don't know how to optimise the `tssRegion` parameter. `c(-1000, 1000)` or `c(-3000, 3000)` are commonly used for human. You may need to checkout some references for your species. Yes, `genomicAnnotationPriority` parameter will affect the priority of genomic annotation and you can set lower priori ...
written 5 days ago by Guangchuang Yu1.5k
2
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1
answer
139
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Answer: A: Chip-seq peak annotation [Chipseeker]
... For virus/bacteria, `tssRegion=c(-3000, 3000)` is too large. ...
written 5 days ago by Guangchuang Yu1.5k
0
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2
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903
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2
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Comment: C: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualiz
... using ```r rvcheck::update_all() ``` to update all your pkgs. ...
written 5 weeks ago by Guangchuang Yu1.5k
0
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2
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903
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2
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Comment: C: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualiz
... see step 1 in . Your installation are too old, in which no `as.data.frame` method defined for `enrichResult`. ...
written 5 weeks ago by Guangchuang Yu1.5k
0
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1
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948
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1
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Comment: C: Phylogenetic tree for viruses
... yes, using phyml or raxml with GTR model make more sense. ...
written 5 weeks ago by Guangchuang Yu1.5k
1
vote
2
answers
622
views
2
answers
Answer: A: organism choose of clusterProfiler
... If using the gene IDs you provided, it should not works for `hsa` as these gene IDs are not belong to human. ``` > g [1] "33157" "3772540" "33202" "33374" "53544" "33396" > select(org.Hs.eg.db, keys=g, keytype="ENTREZID", columns='ENTREZID') Error in .testForValidKeys(x, keys, keytype ...
written 9 weeks ago by Guangchuang Yu1.5k
0
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1
answer
213
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1
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Answer: A: Genomic overlap using ChIPseeker enrichPeakOverlap
... `intersect(peaks1, peaks2)` will give you the overlap. ...
written 10 weeks ago by Guangchuang Yu1.5k
0
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1
answer
197
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1
answers
Answer: A: How to add column name in facet_plot of ggtree
... see ...
written 10 weeks ago by Guangchuang Yu1.5k
0
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2
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903
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2
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Comment: C: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualiz
... From KEGG website. You should know these ID better than me as this is the species you are studying. ...
written 11 weeks ago by Guangchuang Yu1.5k
0
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2
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903
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Comment: C: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualiz
... gene ID not match, as indicated in the **message**. ``` > xx$dme00051 [1] "Dmel_CG10638" "Dmel_CG10688" "Dmel_CG10863" "Dmel_CG1129" "Dmel_CG12289" [6] "Dmel_CG12766" "Dmel_CG1982" "Dmel_CG2171" "Dmel_CG3001" "Dmel_CG31692" [11] "Dmel_CG32849" "Dmel_CG33102" "Dmel_CG3400" "Dmel_CG3495" " ...
written 12 weeks ago by Guangchuang Yu1.5k

Latest awards to Guangchuang Yu

Appreciated 5 weeks ago, created a post with more than 5 votes. For A: specific string extraction use excel, R or Python
Popular Question 12 weeks ago, created a question with more than 1,000 views. For clusterProfiler: an R package for comparing biological themes among gene clusters
Popular Question 4 months ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Scholar 5 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
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Scholar 8 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
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Scholar 9 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
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