User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.1k
Reputation:
1,080
Status:
Trusted
Location:
China/Guangzhou/Southern Medical University
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
7 years, 3 months ago
Email:
g************@gmail.com

Bioinformatics Professor at Southern Medical University.

Posts by Guangchuang Yu

<prev • 305 results • page 1 of 31 • next >
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Comment: C: gseDO function input
... no, see . ...
written 5 weeks ago by Guangchuang Yu1.1k
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Answer: C: Is it possible to run gseDO for mouse 'org.Mm.eg.db'
... No. We may extend it to support mouse in future. But currently Disease Ontology only supports human. ...
written 5 weeks ago by Guangchuang Yu1.1k
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Comment: C: clusterProfiler: BgRatio N value does not equal set gene universe size
... many software do the wrong things to give you smaller p values, but `clusterProfiler` do not. ...
written 6 weeks ago by Guangchuang Yu1.1k
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Answer: A: clusterProfiler: BgRatio N value does not equal set gene universe size
... the secret is here, . If the provided universe contains genes that have no annotation, they will be filtered out. Otherwise, it will downgrade the p value. ...
written 6 weeks ago by Guangchuang Yu1.1k
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Comment: C: how to add background gene set to enrichMesh
... already answer in . ...
written 4 months ago by Guangchuang Yu1.1k
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Answer: A: Highligting specific tips/taxa with asterisk using ggtree
... something like this to add another layer of tip labels, (whether "*" or ""). ...
written 6 months ago by Guangchuang Yu1.1k
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Comment: C: Is compareCluster() reproducible?
... any reproducible example? ...
written 6 months ago by Guangchuang Yu1.1k
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Answer: A: error in keytype performing "enrichGO" from clusterprofiler
... `get_GO_data` need to query "GOALL", "ONTOLOGYALL" from `OrgDb` and it seems your OrgDb doesn't contain such information. BTW: You can use `enricher` to perform GO analysis without using `OrgDb`. ...
written 8 months ago by Guangchuang Yu1.1k
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Answer: C: How to change the siez of lables in heatmap
... pls refer to the ggplot2 theme reference, . ...
written 9 months ago by Guangchuang Yu1.1k
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Answer: A: kegg enrichment using clusterProfiler could not read KEGG Orthology IDs
... >keggID <- c("K15179", "K03377") > x <- enrichKEGG(keggID, organism='ko', keyType='kegg') >--> No gene can be mapped.... > --> Expected input gene ID: K10780,K16305,K08093,K14275,K18819,K22554 > --> return NULL... Usually, this means that you are using the wrong ID. ...
written 10 months ago by Guangchuang Yu1.1k

Latest awards to Guangchuang Yu

Guru 13 months ago, received more than 100 upvotes.
Scholar 15 months ago, created an answer that has been accepted. For A: ReactomePA - Pathway analysis for DE porcine genes
Teacher 15 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?
Teacher 17 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 2.4 years ago, created an answer that has been accepted. For A: clusterprofiler KEGG enrichment for arabidopsis
Scholar 2.4 years ago, created an answer that has been accepted. For A: Clusterprofiler - MSigDB gene set analysis - Updated
Scholar 2.4 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 2.4 years ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 2.4 years ago, created an answer that has been accepted. For A: Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and m
Teacher 2.4 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?
Supporter 2.4 years ago, voted at least 25 times.
Scholar 2.4 years ago, created an answer that has been accepted. For A: ReactomePA - Pathway analysis for DE porcine genes
Scholar 2.4 years ago, created an answer that has been accepted. For A: clusterProfiler for Zebrafish (Danio rerio)
Scholar 2.4 years ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Scholar 2.7 years ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Centurion 3.6 years ago, created 100 posts.
Scholar 3.6 years ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Scholar 3.6 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 3.6 years ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 3.6 years ago, created an answer that has been accepted. For A: #clusterProfiler# KEGG enrichment with non-reference species
Scholar 3.6 years ago, created an answer that has been accepted. For A: ChIPseeker question: provide custom csAnno to plots
Popular Question 3.6 years ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 3.8 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Teacher 3.8 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?

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