User: Guangchuang Yu

gravatar for Guangchuang Yu
Guangchuang Yu1.4k
Reputation:
1,350
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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:
6 hours ago
Joined:
5 years, 3 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 • 135 results • page 1 of 14 • next >
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Comment: C: how to give column names for a data in R
... ```r nms <- readLines("your_file_that_stores_colname_one_at_each_line") colnames(data) <- nms ``` ...
written 4 days ago by Guangchuang Yu1.4k
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Answer: A: Is it possible to recreate clusterProfiler plots using my own pathway data?
... maybe you can try `merge_result` function, see and corresponding source code in . ...
written 28 days ago by Guangchuang Yu1.4k
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210
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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 4 weeks ago by Guangchuang Yu1.4k
1
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1
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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 5 weeks ago by Guangchuang Yu1.4k
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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 You must install an outdated versioin.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 5 weeks ago by Guangchuang Yu1.4k
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1
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Answer: A: ggtree "open_tree" not found in linux version
... see . ...
written 5 weeks ago by Guangchuang Yu1.4k
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1.1k
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Comment: C: ggtree: phylogenetic tree visualization and annotation
... pls google search it before posting question. see . ...
written 6 weeks ago by Guangchuang Yu1.4k
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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 6 weeks ago by Guangchuang Yu1.4k
1
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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 6 weeks ago by Guangchuang Yu1.4k
3
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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 7 weeks ago by Guangchuang Yu1.4k

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