User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.1k
Reputation:
1,070
Status:
Trusted
Location:
China/Guangzhou/Southern Medical University
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 1 day ago
Joined:
6 years, 8 months ago
Email:
g************@gmail.com

Bioinformatics Professor at Southern Medical University.

Posts by Guangchuang Yu

<prev • 298 results • page 1 of 30 • next >
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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 22 days 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 7 weeks 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 9 weeks ago by Guangchuang Yu1.1k
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Comment: C: MeSH enrichment analysis with "meshes"
... what's the output of `traceback()` immediately run after the error appear? ...
written 10 weeks ago by Guangchuang Yu1.1k
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Comment: C: Gene similarity by GOSemSim
... pls provide `k` to make your code reproducible. ...
written 11 weeks ago by Guangchuang Yu1.1k
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Comment: C: how to get frequencies from plotDistToTSS
... as the output is a ggplot object, you can try: p <- plotDistToTSS(...) p$data The p$data should contains relative information. ​ ...
written 3 months ago by Guangchuang Yu1.1k
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Comment: C: Semantic similarity across entire MeSH tree in meshes pkg
... mixed category is not supported, similar to BP, CC and MF of GO. You should separate and analysis respectively. ...
written 3 months ago by Guangchuang Yu1.1k
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Comment: C: How to convert data frame obtained with enrichPathway back to an enrichPathway r
... you should emapplot(x) but not using x@result. ​ ...
written 3 months ago by Guangchuang Yu1.1k
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Answer: A: How to convert data frame obtained with enrichPathway back to an enrichPathway r
... x@result = x@result[x@result$ID %in% your_id_list, ] ​ ...
written 3 months ago by Guangchuang Yu1.1k
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Comment: C: How can I read in BEAST nexus tree with treeio and get all node values
... thanks for sending the file. I have no problem to read the file using treeio package. > require(treeio) > phyA <- read.beast("bk98_01_11_A7.tre") > require(tidytree) > d <- as_tibble(phyA) > d[69,'length_0.95_HPD'] # A tibble: 1 x 1 length_0.95_HPD <list> ...
written 3 months ago by Guangchuang Yu1.1k

Latest awards to Guangchuang Yu

Guru 5 months ago, received more than 100 upvotes.
Scholar 7 months ago, created an answer that has been accepted. For A: ReactomePA - Pathway analysis for DE porcine genes
Teacher 7 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 9 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: clusterprofiler KEGG enrichment for arabidopsis
Scholar 21 months ago, created an answer that has been accepted. For A: Clusterprofiler - MSigDB gene set analysis - Updated
Scholar 21 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 21 months ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 21 months ago, created an answer that has been accepted. For A: Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and m
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?
Supporter 21 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: ReactomePA - Pathway analysis for DE porcine genes
Scholar 21 months ago, created an answer that has been accepted. For A: clusterProfiler for Zebrafish (Danio rerio)
Scholar 21 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Centurion 2.9 years ago, created 100 posts.
Scholar 2.9 years ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Scholar 2.9 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 2.9 years ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 2.9 years ago, created an answer that has been accepted. For A: #clusterProfiler# KEGG enrichment with non-reference species
Scholar 2.9 years ago, created an answer that has been accepted. For A: ChIPseeker question: provide custom csAnno to plots
Popular Question 2.9 years ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 3.2 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Teacher 3.2 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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