User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.1k
Reputation:
1,050
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, 3 months ago
Email:
g************@gmail.com

Bioinformatics Professor at Southern Medical University.

Posts by Guangchuang Yu

<prev • 285 results • page 1 of 29 • next >
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Comment: C: No gene set have size > 10 ...
... you are correct, as the source code indicated: idx <- minGSSize <= geneSet_size & geneSet_size <= maxGSSize ​ ​ ...
written 22 days ago by Guangchuang Yu1.1k
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Comment: C: No gene set have size > 10 ...
... any reproducible example? ...
written 23 days ago by Guangchuang Yu1.1k
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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 weeks ago by Guangchuang Yu1.1k
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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 3 months ago by Guangchuang Yu1.1k
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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 4 months ago by Guangchuang Yu1.1k
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Comment: C: Error Installing Cluster Profiler
... see https://github.com/GuangchuangYu/DOSE/issues/25#event-1666307599. ​ ...
written 4 months ago by Guangchuang Yu1.1k
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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 4 months ago by Guangchuang Yu1.1k
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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 4 months ago by Guangchuang Yu1.1k
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Comment: C: ReactomePA / Reactome: Crash when plotting
... ...
written 5 months ago by Guangchuang Yu1.1k
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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 5 months ago by Guangchuang Yu1.1k

Latest awards to Guangchuang Yu

Guru 6 weeks ago, received more than 100 upvotes.
Scholar 3 months ago, created an answer that has been accepted. For A: ReactomePA - Pathway analysis for DE porcine genes
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?
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?
Scholar 16 months ago, created an answer that has been accepted. For A: clusterprofiler KEGG enrichment for arabidopsis
Scholar 16 months ago, created an answer that has been accepted. For A: Clusterprofiler - MSigDB gene set analysis - Updated
Scholar 16 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 16 months ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 16 months ago, created an answer that has been accepted. For A: Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and m
Teacher 16 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 16 months ago, voted at least 25 times.
Scholar 16 months ago, created an answer that has been accepted. For A: ReactomePA - Pathway analysis for DE porcine genes
Scholar 16 months ago, created an answer that has been accepted. For A: clusterProfiler for Zebrafish (Danio rerio)
Scholar 16 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Scholar 20 months ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Popular Question 21 months ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Centurion 2.6 years ago, created 100 posts.
Scholar 2.6 years ago, created an answer that has been accepted. For A: Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
Scholar 2.6 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 2.6 years ago, created an answer that has been accepted. For A: Sort clusterProfiler result
Scholar 2.6 years ago, created an answer that has been accepted. For A: #clusterProfiler# KEGG enrichment with non-reference species
Scholar 2.6 years ago, created an answer that has been accepted. For A: ChIPseeker question: provide custom csAnno to plots
Popular Question 2.6 years ago, created a question with more than 1,000 views. For new package `ggtree` in devel branch
Scholar 2.8 years ago, created an answer that has been accepted. For A: GOSemSim problem for yeast proteins
Teacher 2.8 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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