User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.0k
Reputation:
1,010
Status:
Trusted
Location:
Hong Kong
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
5 days, 19 hours ago
Joined:
5 years, 11 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 • 281 results • page 1 of 29 • next >
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Comment: C: How to save changes on a phylogeneitc tree using ggtree and treeio?
... duplicated, see <https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/UeLEdMYndrA/hZghmSkUCwAJ>. ...
written 7 days ago by Guangchuang Yu1.0k
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Comment: C: Error Installing Cluster Profiler
... see https://github.com/GuangchuangYu/DOSE/issues/25#event-1666307599. ​ ...
written 25 days ago by Guangchuang Yu1.0k
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Comment: C: How does vennplot() within Chipseeker define overlaps?
... I think the answer should be yes. The overlap was calculated via GenomicRanges::intersect. ​ ...
written 26 days ago by Guangchuang Yu1.0k
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Comment: C: GO similarity by GOSemSim
... > select(org.Hs.eg.db, keys = genes, "GO", keytype = "UNIPROT") Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'UNIPROT'. Please use the keys method to see a listing of valid arguments. > genes [1] "P25044" "P40454" "P32901" "P43606" ​ ...
written 27 days ago by Guangchuang Yu1.0k
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Comment: C: ReactomePA / Reactome: Crash when plotting
... ...
written 4 weeks ago by Guangchuang Yu1.0k
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Comment: C: ReactomePA / Reactome: Crash when plotting
...   > res <- lapply(dataSets, function(dataSet) { + data <- read.table(dataSet, header=T) + enrichPathway(data$x, organism = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2) + }) > emp = lapply(res, emapplot) > cowplot::plot_grid(plotlist=emp, ncol=2) ​ can ...
written 4 weeks ago by Guangchuang Yu1.0k
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Comment: C: Remove highly similar terms from a GO gene set enrichment analysis
... will implement the method for gseGO output in future release. ...
written 4 weeks ago by Guangchuang Yu1.0k
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Comment: C: ReactomePA / Reactome: Crash when plotting
... pls make sure you are using latest release version.   If the issue still exists when using latest release version, pls provide reproducible example.   ...
written 4 weeks ago by Guangchuang Yu1.0k
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Comment: C: clusterProfiler: exclude pathways and add gene names to cnetplot
... pls use enrichplot v >= 1.0.2 or v >= 1.1.2, which address the issue you reported. you misunderstand how setReadable works. ## run gseKEGG as usual kk <- gseKEGG() ## convert gene ID to symbol kk2 <- setReadable(kk) # refer to man for additional parameters ## plot cn ...
written 6 weeks ago by Guangchuang Yu1.0k
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Answer: A: clusterProfiler: exclude pathways and add gene names to cnetplot
... 1. same question posted on https://github.com/GuangchuangYu/DOSE/issues/20#issuecomment-391802809​. please upgrade enrichplot to v >= 1.0.1, and then you can pass selected Pathway Names (selected from the Description column) to showCategory parameter.   2. you can use DOSE::setReadable to tran ...
written 6 weeks ago by Guangchuang Yu1.0k

Latest awards to Guangchuang Yu

Scholar 12 months ago, created an answer that has been accepted. For A: clusterprofiler KEGG enrichment for arabidopsis
Scholar 12 months ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 12 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Scholar 12 months ago, created an answer that has been accepted. For A: Clusterprofiler - MSigDB gene set analysis - Updated
Teacher 12 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?
Supporter 12 months ago, voted at least 25 times.
Scholar 12 months ago, created an answer that has been accepted. For A: Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and m
Scholar 12 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 12 months ago, created an answer that has been accepted. For A: clusterProfiler for Zebrafish (Danio rerio)
Scholar 12 months ago, created an answer that has been accepted. For A: ReactomePA - Pathway analysis for DE porcine genes
Scholar 16 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Popular Question 17 months ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Centurion 2.2 years ago, created 100 posts.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 2.2 years ago, created an answer that has been accepted. For A: ChIPseeker question: provide custom csAnno to plots
Scholar 2.2 years ago, created an answer that has been accepted. For A: #clusterProfiler# KEGG enrichment with non-reference species
Scholar 2.2 years ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 2.2 years 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 2.2 years ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Teacher 2.5 years 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 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
Scholar 2.8 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 3.2 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 3.4 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins

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