User: Luo Weijun

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Luo Weijun1.4k
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Posts by Luo Weijun

<prev • 186 results • page 1 of 19 • next >
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Answer: A: Pathview: visualization of data
... Michaela, Thanks for your interest in Pathview. Question 1: you can set limit=list(gene=c(0,100), cpd=1) with your pathview() call. Question 2: you need to do pathway analysis to select significantly perturbed pathway first, you may tools like gage: http://bioconductor.org/packages/release/bioc/h ...
written 4 days ago by Luo Weijun1.4k
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Answer: A: Pathview pathview kegg.native=TRUE throws error in img
... Does this error only occur to pathway 04215 or other pathways too, only with this data or other data too? ...
written 23 days ago by Luo Weijun1.4k
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Answer: A: Can edgeR be used on GO terms?
... You may use gage package for GO and pathway analysis. http://bioconductor.org/packages/release/bioc/html/gage.html http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf ...
written 27 days ago by Luo Weijun1.4k
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Job: Research Scientist in Biostatistics/Bioinformatics
... UNC Charlotte Dept. of Bioinformatics is seeking a full time research scientist in Biostatistics/Bioinformatics. The incumbent will develop statistical/computational methods/tools for high throughput omics (genome, transcriptome, proteome, metabolome etc) data integration, analysis and visualization ...
genetics job statistics R genomics written 5 weeks ago by Luo Weijun1.4k
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Job: Full Time Bioinformatics Software Developer
... UNC Charlotte Dept. of Bioinformatics is seeking a full time Software Developer (research associate). The incumbent will lead the development of bioinformatics web servers, resources and applications. He/she will also work on big data integration and analysis. One focus is the Pathview project. Path ...
job rmysql R php javascript written 5 weeks ago by Luo Weijun1.4k
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Answer: A: Error: Pathway analysis using Sleuth results
... if you got pathway graphs with no color, then your data were not mapped to the target pathways. It could be that you specify the wrong species or gene ID, or your data are in the wrong format. First of all, your species is Rrr, what’s that, this is not a KEGG species! Your gene ID map used some pac ...
written 10 weeks ago by Luo Weijun1.4k
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Comment: C: Questions about Pathview, maybe also gage
... comments deleted ...
written 10 weeks ago by Luo Weijun1.4k
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Answer: A: GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
... You should do something like: ref.idx=1 samp.idx=2 cnts.kegg.p <- gage(cnts.norm, gsets = kegg.gs, ref= ref.idx, samp = samp.idx) ...
written 3 months ago by Luo Weijun1.4k
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Answer: A: GO slim data for GAGE GSEA analysis
... gage package does provide a function, esset.grp(), to extract a non-redundant signcant gene set list and related data from gage() results. For details: library(gage) ?esset.grp ...
written 4 months ago by Luo Weijun1.4k
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Answer: A: How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow
... I guess you are following the code from gage tutorial section “8 Result Presentation and Intepretation” after you are done with the code from RNA-Seq workflow tutorial. They are not really meant to be used together directly. You can check the documentation for function essGene() by: ? essGene It wor ...
written 4 months ago by Luo Weijun1.4k

Latest awards to Luo Weijun

Scholar 2.3 years ago, created an answer that has been accepted. For A: Output from pathview does not seem to match input
Scholar 2.3 years ago, created an answer that has been accepted. For A: embed url in pathview images
Scholar 2.3 years ago, created an answer that has been accepted. For A: Pathview: Exporting non native KEGG pathway to PNG
Popular Question 2.3 years ago, created a question with more than 1,000 views. For GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
Centurion 2.5 years ago, created 100 posts.

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