User: bigmawen

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bigmawen270
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Posts by bigmawen

<prev • 34 results • page 1 of 4 • next >
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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 11 weeks ago by bigmawen270
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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 11 weeks ago by bigmawen270
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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 12 weeks ago by bigmawen270
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Job: Postdoc and PhD student with statistics/analytics training at UNC Charlotte, NC, USA
... UNC Charlotte Dept. of Bioinformatics is seeking new members as postdoc researchers and PhD students. The incumbent 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 and ...
omics statistics job R bioinformatics big data written 5 months ago by bigmawen270
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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 7 months ago by bigmawen270
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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 15 months ago by bigmawen270
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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 16 months ago by bigmawen270
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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 16 months ago by bigmawen270
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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 16 months ago by bigmawen270
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Tool: Pathview Web server published in NAR
... The Pathview Web server was recently published in Nucleic Acids Research (NAR) Web Server issue: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx372 Pathview is an R/Bioconductor package for pathway based data integration and visualization. It maps and renders a wide variety of biolo ...
omics visualization pathway analysis rna-seq tool written 16 months ago by bigmawen270

Latest awards to bigmawen

Scholar 24 months ago, created an answer that has been accepted. For A: GAGE - eg2sym (ID conversion)
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: GAGE - eg2sym (ID conversion)

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