Posts Tagged ‘ Pathways ’

Tutorial: RNA-seq differential expression & pathway analysis with Sailfish, DESeq2, GAGE, and Pathview

December 4, 2015
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BackgroundThis tutorial shows an example of RNA-seq data analysis with DESeq2, followed by KEGG pathway analysis using GAGE. Using data from GSE37704, with processed data available on Figshare DOI: 10.6084/m9.figshare.1601975. This dataset has six samp...

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Russ Altman’s Translational Bioinformatics Year in Review

April 22, 2014
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Russ Altman’s Translational Bioinformatics Year in Review

A few weeks ago the 2014 AMIA Translational Bioinformatics Meeting (TBI) was held in beautiful San Francisco.  This meeting is full of great science that spans the divide between molecular and clinical research, but a true highlight of this meetin...

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NetGestalt for Data Visualization in the Context of Pathways

February 20, 2013
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NetGestalt for Data Visualization in the Context of Pathways

Many of you may be familiar with WebGestalt, a wonderful web utility developed by Bing Zhang at Vanderbilt for doing basic gene-set enrichment analyses. Last year, we invited Bing to speak at our annual retreat for the Vanderbilt Graduate Program in H...

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Pathway Analysis for High-Throughput Genomics Studies

March 6, 2012
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Pathway Analysis for High-Throughput Genomics Studies

I get a lot of requests in the core about running a "pathway analysis." Someone ran a handful of gene expression arrays, or better yet, ran an RNA-seq experiment (with replicates!). These, and many other kinds of high-throughput assays (GWAS, ChIP-seq,...

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