User: Guangchuang Yu

gravatar for Guangchuang Yu
Reputation:
700
Status:
Trusted
Location:
Hong Kong
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
1 week, 1 day ago
Joined:
5 years, 2 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 • 229 results • page 1 of 23 • next >
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Comment: C: clusterProfiler enrichGO under-represented term
... No. currently only over-representation is supported. ...
written 8 days ago by Guangchuang Yu700
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Answer: A: ggtree: time-scaled tree s
... Then proceeded to calibrate that tree with the ages from the table. Do you mean you are using the paleotree to infer time to MRCA? I don’t know the paleotree package, but if it can be used to process your data and give you the time-scaled tree, then you can use it and using ggtree to visualize the ...
written 6 weeks ago by Guangchuang Yu700
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Answer: A: clusterProfiler: different runs return different results for gse functions
... The results are similar from the outputs pasted here. It would be better if you can calculate the overlap enriched term and compare the pvalue similar to what I did in http://guangchuangyu.github.io/2015/11/comparison-of-clusterprofiler-and-gsea-p/ . ​ On Tue, Aug 29, 2017 at 10:23 PM, ssv [bioc] ...
written 7 weeks ago by Guangchuang Yu700
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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 9 weeks ago by Guangchuang Yu700
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Answer: A: gseDO function input
... see https://github.com/GuangchuangYu/DOSE/wiki/how-to-prepare-your-own-geneList. ​ ...
written 9 weeks ago by Guangchuang Yu700
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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 9 weeks ago by Guangchuang Yu700
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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 3 months ago by Guangchuang Yu700
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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 3 months ago by Guangchuang Yu700
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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 3 months ago by Guangchuang Yu700
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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 3 months ago by Guangchuang Yu700

Latest awards to Guangchuang Yu

Scholar 7 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Popular Question 8 months ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 18 months ago, created an answer that has been accepted. For A: ChIPseeker question: provide custom csAnno to plots
Popular Question 18 months ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 18 months ago, created an answer that has been accepted. For A: #clusterProfiler# KEGG enrichment with non-reference species
Scholar 18 months ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 18 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 18 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Centurion 18 months ago, created 100 posts.
Teacher 21 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 21 months ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 24 months ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 2.0 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
Scholar 2.7 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Autobiographer 2.9 years ago, has more than 80 characters in the information field of the user's profile.

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