User: Guangchuang Yu

gravatar for Guangchuang Yu
Reputation:
690
Status:
Trusted
Location:
Hong Kong
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
23 hours ago
Joined:
5 years 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 • 226 results • page 1 of 23 • next >
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Comment: C: clusterProfiler - interpretation of enrichMap
... Currently, the only possibility is to save the enrichMap output to a igraph object and then by change the igraph object and re-plot again. ​ ...
written 3 days ago by Guangchuang Yu690
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Answer: A: gseDO function input
... see https://github.com/GuangchuangYu/DOSE/wiki/how-to-prepare-your-own-geneList. ​ ...
written 7 days ago by Guangchuang Yu690
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Comment: C: eroor mssage using gseKEGG
... thanks for your comments. I think I need to update the code to throw more informative error in this case. ...
written 7 days ago by Guangchuang Yu690
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Comment: C: #clusterProfiler# KEGG enrichment with non-reference species
... they are based on the ko database. If you want to use your own data, see http://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/. ​ ...
written 4 weeks ago by Guangchuang Yu690
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Answer: A: ClusterProfiler dotplot formatting
... try: your_dot_plot + ggplot2::xlim(NA, 45) to allocate large space in right hand side. see also https://guangchuangyu.github.io/ggtree/faq/#tip-label-truncated. ​ ...
written 5 weeks ago by Guangchuang Yu690
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Comment: C: odd results "No enrichment found in any of gene cluster"
... yes, and the parameter list of compareCluster depends on the fun parameter. In your case, all enrichKEGG parameters can be passed to compareCluster. ​ ...
written 7 weeks ago by Guangchuang Yu690
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Comment: C: odd results "No enrichment found in any of gene cluster"
... > CompKEGG <- compareCluster(geneCluster = list, fun = "enrichKEGG",organism="hsa", pvalueCutoff=1) Error in compareCluster(geneCluster = list, fun = "enrichKEGG", organism = "hsa", : No enrichment found in any of gene cluster, please check your input... > CompKEGG <- compareCluster ...
written 7 weeks ago by Guangchuang Yu690
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Answer: A: odd results "No enrichment found in any of gene cluster"
... your code is not reproducible. pls see also https://support.bioconductor.org/p/96681/#96687. ​ ...
written 7 weeks ago by Guangchuang Yu690
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Answer: A: Chip-seq peak annotation [Chipseeker]
... For virus, tssRegion=c(-3000, 3000) is too large. ​ ...
written 8 weeks ago by Guangchuang Yu690
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Comment: C: GSEA threshold question
... any reproducible example? ...
written 8 weeks ago by Guangchuang Yu690

Latest awards to Guangchuang Yu

Scholar 5 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Popular Question 6 months ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 16 months ago, created an answer that has been accepted. For A: ChIPseeker question: provide custom csAnno to plots
Popular Question 16 months ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 16 months ago, created an answer that has been accepted. For A: #clusterProfiler# KEGG enrichment with non-reference species
Scholar 16 months ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 16 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 16 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Centurion 16 months ago, created 100 posts.
Teacher 19 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 19 months ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 22 months ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 22 months ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 2.3 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 2.5 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.

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