User: Luo Weijun

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Luo Weijun1.4k
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Posts by Luo Weijun

<prev • 216 results • page 1 of 22 • next >
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Answer: A: Issue with xml files downloaded with `pathview()`
... This does not look like an xml file, and it is not a file pathview downloads. To see what pathview download, try: download.kegg(pathway="04622", species="hsa") you will see two files starts with hsa04622 in your working directory, one of them is xml. ...
written 18 hours ago by Luo Weijun1.4k
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Comment: C: Recent build and parsing error in pathview
... you just need these two lines to install pathview: source("http://bioconductor.org/biocLite.R") biocLite("pathview") This following line installs an old version from R-Forge, likely caused the problem. install.packages("pathview",repos="http://R-Forge.R-project.org") you seemed to copy and p ...
written 5 months ago by Luo Weijun1.4k
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Job: Postdoc and PhD student in Bioinformatics/Biostatistics
... UNC Charlotte Dept. of Bioinformatics is seeking new members as postdoc researchers and PhD students. The incumbent(s) will work on big data integration and analysis, methodology development, and contribute to a range of challenging and important research projects in biomedicine.    We integrate an ...
job statistics R ngs genomics big data written 5 months ago by Luo Weijun1.4k
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Answer: A: KEGG enrichment for non-model
... GAGE will work with your data if you: -change the rowname of your data matrix or the names of your data vector to ko gene ID (keggID in your example) -if the data is fold change already, set both ref and samp to NULL when calling gage function. -follow/understand the tutorial and package document ...
written 12 months ago by Luo Weijun1.4k
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Job: Biostatistics/Bioinformatics Research Scientist
... UNC Charlotte Dept. of Bioinformatics is seeking a full time research scientist in Biostatistics/Bioinformatics. The incumbent will develop statistical and computational methods for big data analysis, integration and visualization. S/he will work on a range of high throughput omics (genome, transcri ...
genetics job statistics R ngs genomics written 12 months ago by Luo Weijun1.4k
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Answer: A: GAGE function and the same.dir option
... same.dir=T tests for pathways with genes changing towards one direction. Greater and less components in the results correspond to tests for up and down regulated pathways respectively. same.dir=F tests for pathways where genes change towards both directions at the same time. There is only greater bu ...
written 14 months ago by Luo Weijun1.4k
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Answer: A: Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad
... you path.ids2 seems to be all NAs, instead of proper KEGG pathway IDs (like 04130, 00120 etc). That's why these non-existing pathway data files could not be downloaded. you should check why NAs were generated ...
written 16 months ago by Luo Weijun1.4k
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Answer: A: Error when installing package gageData
... This is not a gageData specific problem, the installation of other packages failed too in your output. Your code is not consistent with the output either. You code only install gageData, but output shows that other packages were also being installed, and pathview package was loaded somehow. ...
written 17 months ago by Luo Weijun1.4k
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pathview and gage server connection issue
... Dear pathview and gage user,  Recent versions of both packages connect to the Pathview Web server for updated KEGG data. The Pathview server is not accessible in 2/12-2/13. You may experience issues in loading the package or using some functions. Please update your pathview and gage packages to the ...
visualization gage pathview kegg pathway analysis written 17 months ago by Luo Weijun1.4k
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Answer: A: Highlight ECs by KEGG module
... You can definitely visualize/highlight just ECs/genes/nodes from a particular module. In you case, you can do something like: library(pathview) library(KEGGREST) m1=keggLink("ko","M00039") m1=gsub("ko:", "", m1) pv.out <- pathview(gene.data = m1, pathway.id = "00940", out.suffix = "toy.examp ...
written 20 months ago by Luo Weijun1.4k

Latest awards to Luo Weijun

Popular Question 6 months ago, created a question with more than 1,000 views. For Pathview for global and overview maps Re: using pathview about hsa01100
Popular Question 6 months ago, created a question with more than 1,000 views. For GAGE/Pathview analysis data preparation
Popular Question 6 months ago, created a question with more than 1,000 views. For Pathview question
Popular Question 6 months ago, created a question with more than 1,000 views. For Pathview with non-KEGG organisms?
Popular Question 6 months ago, created a question with more than 1,000 views. For DESeq2 with GAGE
Popular Question 6 months ago, created a question with more than 1,000 views. For pathview -- ID Problem?
Popular Question 8 months ago, created a question with more than 1,000 views. For Pathview with non-KEGG organisms?
Popular Question 10 months ago, created a question with more than 1,000 views. For Pathview with non-KEGG organisms?
Popular Question 16 months ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Popular Question 16 months ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Workflows: reference genome issue
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Pathview with non-KEGG organisms?
Scholar 2.1 years ago, created an answer that has been accepted. For A: embed url in pathview images
Scholar 2.1 years ago, created an answer that has been accepted. For A: Output from pathview does not seem to match input
Popular Question 2.1 years ago, created a question with more than 1,000 views. For DESeq2 with GAGE
Popular Question 2.1 years ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Scholar 4.6 years ago, created an answer that has been accepted. For A: Pathview: Exporting non native KEGG pathway to PNG
Scholar 4.6 years ago, created an answer that has been accepted. For A: embed url in pathview images
Scholar 4.6 years ago, created an answer that has been accepted. For A: Output from pathview does not seem to match input
Popular Question 4.6 years ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Centurion 4.9 years ago, created 100 posts.

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