User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.6k
Reputation:
1,580
Status:
Trusted
Location:
China/Hong Kong/The University of Hong Kong
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
2 hours ago
Joined:
5 years, 9 months ago
Email:
g************@gmail.com

I study Systems Biology at The University of Hong Kong.

Email: guangchuangyu@gmail.com

Posts by Guangchuang Yu

<prev • 150 results • page 1 of 15 • next >
2
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Answer: A: GO enrichment - interpreting broad terms
... using [simplify](https://guangchuangyu.github.io/2015/10/use-simplify-to-remove-redundancy-of-enriched-go-terms/) in [clusterProfiler](https://guangchuangyu.github.io/clusterProfiler/) to remove redundancy and help interpretation of GO enrichment result. ...
written 5 weeks ago by Guangchuang Yu1.6k
0
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3
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217
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3
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Answer: A: can you calculate GO enrichment from GO terms and IDs?
... [clusterProfiler](https://guangchuangyu.github.io/clusterProfiler/) support using [user's own annotation](http://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/). The package is quite popular and has been cited by >200 papers. ...
written 6 weeks ago by Guangchuang Yu1.6k
2
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1
answer
234
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1
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Comment: C: Chip-seq peak annotation [Chipseeker]
... I don't know how to optimise the `tssRegion` parameter. `c(-1000, 1000)` or `c(-3000, 3000)` are commonly used for human. You may need to checkout some references for your species. Yes, `genomicAnnotationPriority` parameter will affect the priority of genomic annotation and you can set lower priori ...
written 9 weeks ago by Guangchuang Yu1.6k
2
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1
answer
234
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1
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Answer: A: Chip-seq peak annotation [Chipseeker]
... For virus/bacteria, `tssRegion=c(-3000, 3000)` is too large. ...
written 9 weeks ago by Guangchuang Yu1.6k
0
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2
answers
1.1k
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2
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Comment: C: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualiz
... using ```r rvcheck::update_all() ``` to update all your pkgs. ...
written 3 months ago by Guangchuang Yu1.6k
0
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2
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1.1k
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Comment: C: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualiz
... see step 1 in . Your installation are too old, in which no `as.data.frame` method defined for `enrichResult`. ...
written 3 months ago by Guangchuang Yu1.6k
0
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1
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1.1k
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1
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Comment: C: Phylogenetic tree for viruses
... yes, using phyml or raxml with GTR model make more sense. ...
written 3 months ago by Guangchuang Yu1.6k
1
vote
2
answers
716
views
2
answers
Answer: A: organism choose of clusterProfiler
... If using the gene IDs you provided, it should not works for `hsa` as these gene IDs are not belong to human. ``` > g [1] "33157" "3772540" "33202" "33374" "53544" "33396" > select(org.Hs.eg.db, keys=g, keytype="ENTREZID", columns='ENTREZID') Error in .testForValidKeys(x, keys, keytype ...
written 4 months ago by Guangchuang Yu1.6k
0
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1
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278
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1
answers
Answer: A: Genomic overlap using ChIPseeker enrichPeakOverlap
... `intersect(peaks1, peaks2)` will give you the overlap. ...
written 4 months ago by Guangchuang Yu1.6k
0
votes
1
answer
269
views
1
answers
Answer: A: How to add column name in facet_plot of ggtree
... see ...
written 4 months ago by Guangchuang Yu1.6k

Latest awards to Guangchuang Yu

Popular Question 29 days ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Scholar 5 weeks ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Appreciated 3 months ago, created a post with more than 5 votes. For A: specific string extraction use excel, R or Python
Popular Question 4 months ago, created a question with more than 1,000 views. For clusterProfiler: an R package for comparing biological themes among gene clusters
Popular Question 6 months ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Scholar 7 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
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