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Hello! I just started an internship with a bioinformatics group that is currently looking into clinical applications of next generation sequencing technology. One of the projects we’re working on is to sequence someone’s genome and find genes that enable susceptibility to certain diseases, such as cancer. I was wondering if you guys have a recommendation for pathway analysis software. Also, if any of you understand the mechanics of pathway analysis could you please explain to me how it works, or at least direct me to some helpful links? Thanks.
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Hi Pesto,
I hope this will help you out a bit and it's not too late. I'm learning on this too. Just an overview on how it works
Just realized about the question, sorry for the mistake, u can try looking at this website for PathVisio
Dowload available at http://www.pathvisio.org/wiki/PathVisioDownloadLast edited by HuiXin; 05-02-2011, 07:48 PM. -
Hi Pesto,
you might have a look at Genostar, i think they have pathway analysis software. You can download a trial at their website;
BoetsieComment
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One of the fastest most accurate pathway analysis solutions is Ingenuity iReport. Upload your NGS: RNA-Seq Cuff-Diff files at http://www.ingenuity.com/getireport/ and get a free preview of your iReport including pathways, processes, interactions, etc.Comment
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You have only made two posts on SEQanswers and both advertise this report. Please refrain from advertising on the board via posts or your posts might get flagged in the future.Originally posted by bkmacy View PostComment
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Ingenuity looks like a great product for RNAseq pathway analysis but does any similar open course (free) program exist which provides similar analysis results?
Thanks.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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