User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.6k
Reputation:
1,620
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Location:
China/Hong Kong/The University of Hong Kong
Website:
https://guangchuangyu....
Twitter:
guangchuangyu
Scholar ID:
Google Scholar Page
Last seen:
11 hours ago
Joined:
6 years, 1 month ago
Email:
g************@gmail.com

I study Systems Biology at The University of Hong Kong.

Email: guangchuangyu@gmail.com

Posts by Guangchuang Yu

<prev • 155 results • page 1 of 16 • next >
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Answer: A: PANTHER and DAVID can't recognized some Ensembl gene ID?
... > x= 'ENSG00000004660 ENSG00000005249 ENSG00000005448 ENSG00000005486 ENSG00000005812 ENSG00000214548 ENSG00000217325 ENSG00000218416 ENSG00000223839' > id [1] "ENSG00000004660" "ENSG00000005249" "ENSG00000005448" "ENSG00000005486" [5] "ENSG00000005812" "ENSG00000214548" "ENSG ...
written 7 days ago by Guangchuang Yu1.6k
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1
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115
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Answer: A: Error with ecolik12 enrichGO
... answer [here](https://support.bioconductor.org/p/103398/#103399). pls don't create duplicated posts. ...
written 18 days ago by Guangchuang Yu1.6k
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Answer: A: Error while running clusterProfiler
... You did not provide the information of your `org.db` and the error msg indicates that it can't access sqlite file of your `org.db`. ...
written 21 days ago by Guangchuang Yu1.6k
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Answer: A: Pathways visualization for GSEA table input in ClusterProfiler package of Biocon
... clusterProfiler supports GSEA analysis and do provide several visualization methods for GSEA results. If you want to coerce results from other software, there is not such conversion utilities provided. ...
written 5 weeks ago by Guangchuang Yu1.6k
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Answer: A: [ChIPSeeker] Getting overlapping genomic feature annotation (e.g. peak locate in
... there is a `genomicAnnotationPriority` parameter documented in . You can select to report "Rrs1, 3'UTR" OR "Adhfe1, TSS", but and "Rrs1, 3'UTR" & "Adhfe1, TSS" as `annotatePeak` only report the 1st hit according to the annotation priority. Maybe setting the parameter `addFlankGeneInfo = TRUE ...
written 7 weeks ago by Guangchuang Yu1.6k
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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 months ago by Guangchuang Yu1.6k
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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 5 months ago by Guangchuang Yu1.6k
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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 5 months ago by Guangchuang Yu1.6k
2
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1
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377
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Answer: A: Chip-seq peak annotation [Chipseeker]
... For virus/bacteria, `tssRegion=c(-3000, 3000)` is too large. ...
written 5 months ago by Guangchuang Yu1.6k
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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 6 months ago by Guangchuang Yu1.6k

Latest awards to Guangchuang Yu

Popular Question 17 days ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Teacher 10 weeks ago, created an answer with at least 3 up-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 ggtree: phylogenetic tree visualization and annotation
Scholar 5 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Appreciated 6 months ago, created a post with more than 5 votes. For A: specific string extraction use excel, R or Python
Popular Question 8 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 10 months ago, created a question with more than 1,000 views. For ggtree: phylogenetic tree visualization and annotation
Scholar 11 months ago, created an answer that has been accepted. For A: specific string extraction use excel, R or Python
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: specific string extraction use excel, R or Python
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