User: andrew

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andrew460
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4 years, 11 months ago
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Posts by andrew

<prev • 66 results • page 1 of 7 • next >
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Answer: A: What web services can annotate and postprocess a complete human genome VCF comin
... I work for this company, so I am biased. [iVariantGuide][1] is an easy to use web-based tool that takes VCFs as input (4.1 or higher) and will annotate the file and provide graphical filtering and visualizations. It also can produce pathway enrichment analysis, GO analysis, and can produce an auto ...
written 15 months ago by andrew460
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Comment: C: NIH grants - how to acquire body text in addition to just abstracts?
... I'm not aware of any way to programatically get the body of the text you are looking for. I believe you need to request each grant you are interested in through a Freedom of Information Request Act (FOIRA). This happened to us once. Then the PI is usually sent a request where they need to respond ...
written 17 months ago by andrew460
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Comment: C: Some clarification on enrichment analyses and pathway analyses?
... I think Kevin is giving you great advice here! I would add that the underlying assumption in any pathway enrichment analysis is that the genes in the pathway are assumed to be independent variables. In other words, enrichment analysis essentially only "counts" the number of DEGs on a any given p ...
written 19 months ago by andrew460
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Comment: A: How to extract known pathways from protein protein interaction network?
... Your question is not clear. Are you asking if one can extract an ENTIRE pathway from a PPI network? Or are you looking for even PARTIAL pathways from a PPI network - if so, what threshold would you use for inclusion or exclusion? Please restate your question more clearly. ...
written 19 months ago by andrew460
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Comment: C: How do I go from UniProt ID to retrieving the gene name?
... This conversion tool will let you (in theory) a list of unlimited ids, but I think in the UI it is limited to about 3,000. They also have an API that you should be able to access via a terminal and I believe that workflow supports the unlimited workflow. https://biodbnet-abcc.ncifcrf.gov/db/db2db. ...
written 19 months ago by andrew460
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Answer: A: Differential gene expression between a RNA seq and microarray
... Hi Vijay, In [iPathwayGuide][1], we have a feature that allows you to conduct a Meta-Analysis to identify overlapping DEGs across up to 5 separate datasets. The application is agnostic to the platform use to measure expression. I have customers that routinely compare mRNA to protein expression or ...
written 20 months ago by andrew460
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Answer: A: What software with a GUI can compute statistics on a set of VCF NextGene`s outpu
... Have you tried [iVariantGuide][1]? Upload and process your VCF (single or multi-sample) for free. All GUI based. ![enter image description here][2] [1]: https://www.advaitabio.com/ivariantguide.html [2]: https://www.advaitabio.com/uploads/1/6/3/6/16365004/1303209.png ...
written 20 months ago by andrew460
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Comment: C: Many Differentially expressed genes but few GO terms
... By "qval" I assume you mean FDR adjusted p-value. This may be one of the key reasons why your GO analysis is not returning anything significant. FDR is not the best method when looking at ontologies. Read on to see why... Due to the True Path Rule, genes associated with a GO term are also associ ...
written 20 months ago by andrew460
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Answer: A: Doing GSEA analysis on a set of genes
... Please be aware of the severe limitations of GSEA or any enrichment-based analysis. GSEA will only identify those pathways with greater **number** of significant genes (than expected by random chance) and will not help establish if those significant genes are actually contributing or driving a chan ...
written 20 months ago by andrew460
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Answer: A: Is There A Free Alternative To Ingenuity Pathway Analysis?
... As far as I know the only tool that actually uses the FC in the calculation to assess **significance of a pathway** is iPathwayGuide. IPA uses FC to select for DEGs and to perform its upstream regulator analysis, but still relies on an enrichment model to score pathways. ...
written 2.1 years ago by andrew460

Latest awards to andrew

Popular Question 17 months ago, created a question with more than 1,000 views. For iBioGuide: FREE Dedicated Life-Science Relationship Search & Browser
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Is There A Free Alternative To Ingenuity Pathway Analysis?
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Is There A Free Alternative To Ingenuity Pathway Analysis?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: What is the best way to do Pathway Analysis with R?
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: What is the best way to do Pathway Analysis with R?

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