User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.0k
Reputation:
1,030
Status:
Trusted
Location:
China/Guangzhou/Southern Medical University
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
1 week ago
Joined:
6 years, 1 month ago
Email:
g************@gmail.com

Bioinformatics Professor at Southern Medical University.

Posts by Guangchuang Yu

<prev • 283 results • page 1 of 29 • next >
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Answer: A: How to do functional enrichment analysis for only promoter regions using ChIPsee
... > f = getSampleFiles()[[4]] > x = annotatePeak(f, tssRegion=c(-2000, 2000)) >> loading peak file... 2018-09-12 11:19:29 AM >> preparing features information... 2018-09-12 11:19:29 AM >> identifying nearest features... 2018-09-12 11:19:29 AM > ...
written 8 days ago by Guangchuang Yu1.0k
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Answer: A: Understanding clusterprofiler enrichment results
... how can I get the enrichment scores as.data.frame(result) will convert the output to data.frame. ​ ...
written 8 weeks ago by Guangchuang Yu1.0k
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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 10 weeks 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 3 months 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 3 months 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 3 months ago by Guangchuang Yu1.0k
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Comment: C: ReactomePA / Reactome: Crash when plotting
... ...
written 3 months 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 3 months 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 3 months 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 3 months ago by Guangchuang Yu1.0k

Latest awards to Guangchuang Yu

Teacher 3 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 14 months ago, created an answer that has been accepted. For A: clusterprofiler KEGG enrichment for arabidopsis
Scholar 14 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Scholar 14 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
Teacher 14 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 14 months ago, voted at least 25 times.
Scholar 14 months ago, created an answer that has been accepted. For A: Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and m
Scholar 14 months ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 14 months ago, created an answer that has been accepted. For A: Clusterprofiler - MSigDB gene set analysis - Updated
Scholar 14 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: clusterProfiler for Zebrafish (Danio rerio)
Scholar 18 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Popular Question 19 months ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Centurion 2.4 years ago, created 100 posts.
Popular Question 2.4 years ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 2.4 years ago, created an answer that has been accepted. For A: ChIPseeker question: provide custom csAnno to plots
Scholar 2.4 years ago, created an answer that has been accepted. For A: #clusterProfiler# KEGG enrichment with non-reference species
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: 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: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Teacher 2.7 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 2.7 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 2.9 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Scholar 2.9 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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