User: bigmawen

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bigmawen300
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Posts by bigmawen

<prev • 35 results • page 1 of 4 • next >
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Answer: A: Unable to map genes to KEGG pathway using pathview
... Your gene IDs (eg Os03t0659266-00) are not Entrez or KEGG gene ID, hence can’t be mapped to KEGG osa pathways. That’s why you saw the warning and plain graph with no data. you can generate simulated osa data with entrez/kegg ID as below, and it will work. So you need to convert your gene IDs to entr ...
written 6 weeks ago by bigmawen300
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Answer: A: How to perform KEGG enrichment analyses on a set of genes
... You can use gage package in R/Bioconductor: http://bioconductor.org/packages/release/bioc/html/gage.html The K-numbers are KEGG orthology gene IDs. you can generate gene set data for KO using kegg.gsets() function with species='ko'. BTW, KEGG data is constantly updated, so is the gene set data ...
written 5 months ago by bigmawen300
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Job: Research Scientist in Biostatistics/Bioinformatics at UNC Charlotte, NC, USA
... 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 ...
genomics statistics data science job R ngs written 5 months ago by bigmawen300
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Answer: A: Could somebody suggest free pathway visualization tool for omics data from plant
... Pathview maps, integrates and renders a wide variety of biological data on relevant pathway graphs, and produce high quality graphics. Pathview Web server: https://pathview.uncc.edu/ Pathview R/Bioconductor package: http://bioconductor.org/packages/release/bioc/html/pathview.html ...
written 5 months ago by bigmawen300
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Job: Postdoc and PhD student in Bioinformatics/Biostatistics at UNC Charlotte, NC, USA
... 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 a ...
genomics statistics job R ngs big data written 7 months ago by bigmawen300
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News: Pathview Web server down 2/12-2/13 (EST)
... Our computing infrastructure is scheduled for maintenance in the coming week in Monday 2/12 and Tuesday 2/13 (EST). Pathview Web server (https://pathview.uncc.edu) is likely inaccessible at that time. Please make sure to submit your analyses before or after that time window, and keep other users aro ...
pathview web news visualization pathview written 10 months ago by bigmawen300
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Answer: A: What's Pathway Enrichment Analysis?
... As Andrew said, Pathway analysis + data visualization can be done in R/Bioconductor using gage and pathview package. The full workflow is described in their package vignettes: for RNA-Seq data http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf for microar ...
written 18 months ago by bigmawen300
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Answer: A: Is There A Free Alternative To Ingenuity Pathway Analysis?
... Pathview Web server provides a user friendly comprehensive solution for pathway analysis, data integration and visualization. It was recently published in Nucleic Acids Research (NAR) Web Server issue: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx372 Pathview Web server exten ...
written 18 months ago by bigmawen300
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Answer: A: Error: Pathway analysis using Sleuth results
... pathway graphs without data mapped is because that no gene (or compound) IDs can be mapped to the pathways. This is most likely because that gene.idtype (or cpd.idtype) is the not set correctly or gene.data (cpd.data) is not in the right format. The error messages are consistent with this. Please ch ...
written 18 months ago by bigmawen300
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Answer: A: GAGE or GSEABase using expression data and pathway.gmt file for mouse
... Gage package has a tutorial on data preparation, which describes how to read and prepare gene set data in gmt format: http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/dataPrep.pdf GAGE is a gene set/pathway analysis method, which can be applied to RNA-seq data independent of sp ...
written 18 months ago by bigmawen300

Latest awards to bigmawen

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Full Time Bioinformatics Software Developer at UNC Charlotte, NC, USA (updated)
Scholar 5 weeks ago, created an answer that has been accepted. For A: GAGE - eg2sym (ID conversion)
Scholar 2.2 years ago, created an answer that has been accepted. For A: GAGE - eg2sym (ID conversion)
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: GAGE - eg2sym (ID conversion)

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