User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.1k
Reputation:
1,060
Status:
Trusted
Location:
China/Guangzhou/Southern Medical University
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
4 days, 22 hours ago
Joined:
6 years, 6 months ago
Email:
g************@gmail.com

Bioinformatics Professor at Southern Medical University.

Posts by Guangchuang Yu

<prev • 296 results • page 1 of 30 • next >
0
votes
1
answer
91
views
1
answers
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 12 days ago by Guangchuang Yu1.1k
0
votes
0
answers
70
views
0
answers
Comment: C: MeSH enrichment analysis with "meshes"
... what's the output of `traceback()` immediately run after the error appear? ...
written 13 days ago by Guangchuang Yu1.1k
0
votes
0
answers
89
views
0
answers
Comment: C: Gene similarity by GOSemSim
... pls provide `k` to make your code reproducible. ...
written 25 days ago by Guangchuang Yu1.1k
0
votes
0
answers
114
views
0
answers
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 4 weeks ago by Guangchuang Yu1.1k
0
votes
0
answers
87
views
0
answers
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 4 weeks ago by Guangchuang Yu1.1k
0
votes
1
answer
98
views
1
answers
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 5 weeks ago by Guangchuang Yu1.1k
1
vote
1
answer
98
views
1
answers
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 5 weeks ago by Guangchuang Yu1.1k
0
votes
0
answers
82
views
0
answers
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 7 weeks ago by Guangchuang Yu1.1k
0
votes
0
answers
82
views
0
answers
Comment: C: How can I read in BEAST nexus tree with treeio and get all node values
... the last issue is from outbreaktools and/or figtree, you need to open the file with text editor and verify it manually to check whether these program parse the file correctly.   From your msg, treeio fails to parse your file. You can send me the file via email (guangchuangyu AT gmail) and I will l ...
written 7 weeks ago by Guangchuang Yu1.1k
0
votes
1
answer
102
views
1
answers
Answer: A: (GOSemSim package) secondary GO terms generating NA values
... because IC-based methods are species-specific and the GO term is not valid for human. > require(org.Hs.eg.db) > get('GO:0042346', org.Hs.egGO2EG) Error in .checkKeys(value, Rkeys(x), x@ifnotfound) : value for "GO:0042346" not found On Sat, Dec 1, 2018 at 1:05 AM l.willianpacheco [bioc] &l ...
written 7 weeks ago by Guangchuang Yu1.1k

Latest awards to Guangchuang Yu

Guru 3 months ago, received more than 100 upvotes.
Scholar 5 months ago, created an answer that has been accepted. For A: ReactomePA - Pathway analysis for DE porcine genes
Teacher 5 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 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?
Scholar 19 months ago, created an answer that has been accepted. For A: clusterprofiler KEGG enrichment for arabidopsis
Scholar 19 months ago, created an answer that has been accepted. For A: Clusterprofiler - MSigDB gene set analysis - Updated
Scholar 19 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 19 months ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 19 months ago, created an answer that has been accepted. For A: Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and m
Teacher 19 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 19 months ago, voted at least 25 times.
Scholar 19 months ago, created an answer that has been accepted. For A: ReactomePA - Pathway analysis for DE porcine genes
Scholar 19 months ago, created an answer that has been accepted. For A: clusterProfiler for Zebrafish (Danio rerio)
Scholar 19 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Scholar 22 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Popular Question 23 months ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Centurion 2.8 years ago, created 100 posts.
Scholar 2.8 years ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Scholar 2.8 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 2.8 years ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 2.8 years ago, created an answer that has been accepted. For A: #clusterProfiler# KEGG enrichment with non-reference species
Scholar 2.8 years ago, created an answer that has been accepted. For A: ChIPseeker question: provide custom csAnno to plots
Popular Question 2.8 years ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 3.0 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Teacher 3.0 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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 314 users visited in the last hour