User: Guangchuang Yu

gravatar for Guangchuang Yu
Reputation:
970
Status:
Trusted
Location:
Hong Kong
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
4 days, 22 hours ago
Joined:
5 years, 10 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 • 268 results • page 1 of 27 • next >
0
votes
0
answers
77
views
0
answers
Comment: C: Is there a way to set the ClusterProfiler color gradient?
... has changed back to red->blue in 3.8.1 ...
written 4 days ago by Guangchuang Yu970
0
votes
1
answers
66
views
1
answers
Answer: A: How to arrive at an optimal value for attribute level in groupGO or enrichGO in
... I would recommend you using enrichGO function to test whether your genes are significantly related to which GO terms. ​ ...
written 26 days ago by Guangchuang Yu970
0
votes
1
answers
63
views
1
answers
Answer: A: Error in getGenomicAnnoStat(peak.gr) : object 'plab' not found
... fixed in v = 1.15.6 ...
written 5 weeks ago by Guangchuang Yu970
0
votes
1
answers
147
views
1
answers
Answer: A: p-values in Reactome and ReactomePA
... for 2nd issue the result is expected to be different since the p value adjustment rely on the whole set of pvalues while in the 'do it yourself' only a subset was used.   ...
written 7 weeks ago by Guangchuang Yu970
0
votes
1
answers
113
views
1
answers
Answer: A: enrichGO (clusterProfiler) produces different results
... The old version of clusterProfiler has a bug as it take all genes with GO annotation as background. This is why ‘biological process’ can be enriched. This bug has been fixed 1 years ago, and now enrichGO only take all genes with specify sub-GO ontology annotation (e.g. BP). ​ ...
written 8 weeks ago by Guangchuang Yu970
0
votes
1
answers
131
views
1
answers
Answer: A: clusterProfiler for Zebrafish (Danio rerio)
... How can you expect the org.Hs.eg.db (annotation of homo sapiens and only works for human) works with zebrafish? What you need is org.Dr.eg.db. ​ ...
written 9 weeks ago by Guangchuang Yu970
0
votes
1
answers
155
views
1
answers
Answer: A: Clusterprofiler - MSigDB gene set analysis - Updated
... What’s the organism you want to analyze? according to https://www.ncbi.nlm.nih.gov/gene/100516980, it is Sus scrofa. I guess the gmtfile <- "/path/c5.all.v6.1.entrez.gmt" is annotation for human. This is why it throw the msg: --> No gene can be mapped.... --> Expected input gene ID: ...
written 9 weeks ago by Guangchuang Yu970
0
votes
1
answers
216
views
1
answers
Comment: C: ReactomePA - Pathway analysis for DE porcine genes
... maybe you would find the blog post useful. ​ ...
written 9 weeks ago by Guangchuang Yu970
0
votes
1
answers
216
views
1
answers
Answer: A: ReactomePA - Pathway analysis for DE porcine genes
... how about: rpa <- enrichPathway(gene=geneSS, pvalueCutoff=1, qvalueCutoff=1, readable=T, organism="pig") ​ ...
written 9 weeks ago by Guangchuang Yu970
0
votes
1
answers
150
views
1
answers
Comment: C: "input object should be a named list" error in ChIPseeker
... thanks for the recommendation.   In next release, it will throw warning msg (instead of error) that the input should be a named list and set the named automatically. ...
written 9 weeks ago by Guangchuang Yu970

Latest awards to Guangchuang Yu

Scholar 10 months ago, created an answer that has been accepted. For A: clusterprofiler KEGG enrichment for arabidopsis
Scholar 10 months ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 10 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Scholar 10 months ago, created an answer that has been accepted. For A: Clusterprofiler - MSigDB gene set analysis - Updated
Teacher 10 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 10 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For A: Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and m
Scholar 10 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 10 months ago, created an answer that has been accepted. For A: clusterProfiler for Zebrafish (Danio rerio)
Scholar 10 months ago, created an answer that has been accepted. For A: ReactomePA - Pathway analysis for DE porcine genes
Scholar 14 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Popular Question 15 months ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Centurion 2.1 years ago, created 100 posts.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 2.1 years ago, created an answer that has been accepted. For A: ChIPseeker question: provide custom csAnno to plots
Scholar 2.1 years ago, created an answer that has been accepted. For A: #clusterProfiler# KEGG enrichment with non-reference species
Scholar 2.1 years ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 2.1 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 2.1 years ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Teacher 2.3 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 2.3 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 2.6 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 3.1 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 3.3 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 178 users visited in the last hour