User: Guangchuang Yu

gravatar for Guangchuang Yu
Reputation:
810
Status:
Trusted
Location:
Hong Kong
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
9 hours ago
Joined:
5 years, 4 months ago
Email:
g************@gmail.com

I study systems biology at The University of Hong Kong (HKU) as a PhD student and focus my research in evolution of influenza viruses.

Posts by Guangchuang Yu

<prev • 241 results • page 1 of 25 • next >
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Answer: A: Function simplify fails when argument ont is set to "ALL" in enrichGO function i
... It did check whether res@ont %in% c("MF", "BP", "CC") and not support 'ALL' currently. Maybe will support it in future release. ...
written 9 hours ago by Guangchuang Yu810
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Comment: C: clusterProfiler compareCluster enrichDAVID
... any reproducible example of using enrichDAVID that causes Rstudio crash? ...
written 25 days ago by Guangchuang Yu810
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Answer: A: how to define the downstream range in ChIPseeker
... Sorry, it is hard coded. I update the source code in devel branch to support setting the downstream range via: options(ChIPseeker.downstreamDistance = 500) ​ ...
written 28 days ago by Guangchuang Yu810
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Answer: A: enrichGO from DOSE, clusterprofiler is returning empty result.
... see https://github.com/GuangchuangYu/clusterProfiler/wiki/FAQ#no-term-enriched. ​ ...
written 29 days ago by Guangchuang Yu810
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Answer: A: Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and m
... For gene sets with fewer than 10 genes, just 2 or 3 genes can generate significant results. For gene sets larger than 500 genes, they are too general terms and also have a high chance to get significant p values. So these gene sets were eliminated from analysis. The enrichMap only show most signif ...
written 4 weeks ago by Guangchuang Yu810
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Answer: A: ChIPseeker peak annotation tssRegion
... do you have any reproducible example of change the `tssRegion` setting has no effect of the result? ...
written 5 weeks ago by Guangchuang Yu810
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Answer: A: clusterprofiler enrichment analysis geneList argument: duplicate 'row.names' (en
... several different probenames match the same entrezID maybe mean/median value of these probes to assign to the corresponding EntrezID. ​ ...
written 5 weeks ago by Guangchuang Yu810
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Answer: A: question on GO analysis using clusterProfiler
... data(geneList) ego <- enrichGO(gene = gene, universe = names(geneList), OrgDb = org.Mm.eg.db, ... The geneList was obtained via data(geneList), then you are using a vector of human genes as background while testing for mouse gene (Org ...
written 5 weeks ago by Guangchuang Yu810
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Answer: A: chipseeker annotation of focused genic regions
... first exon belongs to exon. first intron belongs to intron. downstream belongs to intergenic. You can simply convert 1st exton to exon etc. ...
written 5 weeks ago by Guangchuang Yu810
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Answer: A: clusterProfiler - Non model organism
... clusterProfiler do support non model organisms. For GO you can use AnnotationHub to query GO annotation. For KEGG, it supports all organisms available in KEGG database as it use the online data, see http://guangchuangyu.github.io/2015/02/kegg-enrichment-analysis-with-latest-online-data-using-cluste ...
written 6 weeks ago by Guangchuang Yu810

Latest awards to Guangchuang Yu

Scholar 9 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Popular Question 10 months ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 20 months ago, created an answer that has been accepted. For A: ChIPseeker question: provide custom csAnno to plots
Popular Question 20 months ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 20 months ago, created an answer that has been accepted. For A: #clusterProfiler# KEGG enrichment with non-reference species
Scholar 20 months ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 20 months ago, created an answer that has been accepted. For A: clusterProfiler : How works the q-value filtering ? What is a good cutoff ? Is t
Scholar 20 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Centurion 20 months ago, created 100 posts.
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: How to do simple Fisher' exact test for overlapped genomic interval in R?
Scholar 23 months ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 2.1 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 2.2 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 2.6 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 2.8 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Autobiographer 3.1 years ago, has more than 80 characters in the information field of the user's profile.

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