User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.3k
Reputation:
1,320
Status:
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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:
3 hours ago
Joined:
5 years, 2 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 • 133 results • page 1 of 14 • next >
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Answer: A: ChIPSeeker - problem with GO enrichment analysis
... pathway.d3TCRp300 <- enrichPathway(gene.d3TCRp300, organism="mouse") You need to have `org.Mm.eg.db` installed. ...
written 1 day ago by Guangchuang Yu1.3k
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Answer: A: Gene set size effect on Gene ontology Semantic Similarity score
... should not have bias on gene set size. please refer to the vignette, which describe the calculation in details. ...
written 7 days ago by Guangchuang Yu1.3k
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Comment: C: ggtree "open_tree" not found in linux version
... you don't need to install devel version for using `open_tree`. You must install an outdated versioin. see and checkout your installation. ...
written 8 days ago by Guangchuang Yu1.3k
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1
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Answer: A: ggtree "open_tree" not found in linux version
... see . ...
written 8 days ago by Guangchuang Yu1.3k
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906
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Comment: C: ggtree: phylogenetic tree visualization and annotation
... pls google search it before posting question. see . ...
written 10 days ago by Guangchuang Yu1.3k
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Comment: C: ggtree: phylogenetic tree visualization and annotation
... that is correct. Actually, you don't need to load `ape` and `ggplot2`. Only `library(ggtree)` would be fine. ...
written 13 days ago by Guangchuang Yu1.3k
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Answer: A: Get all gene symbol in kegg pathway with clusterProfiler
... using github version: ``` > bitr_kegg("hsa04151", "Path", "ncbi-geneid", "hsa") Path ncbi-geneid 1 hsa04151 10000 2 hsa04151 10018 3 hsa04151 100533105 4 hsa04151 10110 5 hsa04151 10161 6 hsa04151 1017 7 hsa04151 1019 8 hsa04151 ...
written 16 days ago by Guangchuang Yu1.3k
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Answer: A: clusterProfiler results problem
... `0`. it would be better if you can tag your post with `clusterprofiler`, so that I can receive email notification. `1`. only set `pvalueCutoff=1` you still get a subset of the result. You need to also set `qvalueCutoff=1`. ```r > tk<- enrichKEGG(gene= gene,organism= 'hsa',pvalueCutoff=1, qva ...
written 20 days ago by Guangchuang Yu1.3k
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10
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Comment: C: Get All The Genes In A Pathway (E.G. Kegg)
... out-dated, see ...
written 22 days ago by Guangchuang Yu1.3k
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Answer: A: out of memory in R after run ChIPSeeker
... @Lila M had sent me the original file which is about 1.2Gb. It's indeed memory intensive in ID converting step. I had optimized this step and it runs more faster and required less memory. The optimized version is available on github: . It only took 19 second to annotate the peaks (31027455 recor ...
written 27 days ago by Guangchuang Yu1.3k

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