User: jared.andrews07

gravatar for jared.andrews07
Reputation:
320
Status:
Trusted
Location:
Washington University in St. Louis
Website:
https://github.com/j-a...
Last seen:
5 hours ago
Joined:
4 months, 3 weeks ago
Email:
j**************@gmail.com

Ph.D. candidate at Washington University in St. Louis. I have a strong interest in the development of high-performance, flexible bioinformatic tools that can integrate multiple -omics datasets to yield interesting and plausible conclusions that can then be experimentally validated.

Avid Python user and fledgling developer. Strange fascination with ostriches.

Posts by jared.andrews07

<prev • 58 results • page 1 of 6 • next >
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Comment: C: Will Python Take The Place Of R?
... Oh, it definitely is. No reason to limit the toolkit. It's funny you mention the syntax, as I find bracket-based syntax infinitely more annoying visually and while writing. I get the advantages, but it just causes headaches for me. I actually agree with your last point, I just find python a lot si ...
written 6 hours ago by jared.andrews07320
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Answer: A: Will Python Take The Place Of R?
... Well, years after the original question, I think this is worth a revisit. While I agree with Kevin's answer fully, it's interesting to see how python has progressed in recent years to catchup with R on the statistical and visualization side of things. As others have mentioned, numpy, pandas, and sci ...
written 13 hours ago by jared.andrews07320
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Comment: C: DiffBind update warnings and running errors
... You'd likely get a quicker response by posting on the [Bioconductor forum][1]. The authors are pretty active there. [1]: https://support.bioconductor.org/ ...
written 2 days ago by jared.andrews07320
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Comment: C: ActiveEnhancers and Gene expression
... You want to do enhancer divergence between species? Which species? Build a model of what? More info will yield better answers as we'll better understand what you're trying to achieve. ...
written 3 days ago by jared.andrews07320
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Comment: C: data mining in bioinformatics
... So what's your question exactly? You can Google 'datamining in bioinformatics' and find dozens of articles, presentations, etc. If you have a specific question, you should edit your original question to include it along with any other information necessary for people to give you an adequate answer. ...
written 4 days ago by jared.andrews07320
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Answer: A: ActiveEnhancers and Gene expression
... There are many different methods/packages for doing things like this out there. A little searching will yield many a blog post, Biostars questions, and publications. My usual workflow for this usually goes something like this: **1.) Identify differentially bound beaks.** Assuming you've already ...
written 7 days ago by jared.andrews07320
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Comment: C: vcf file format
... Have you actually tried whatever you want to do? It may still very well work. The changes in v4.3 aren't all that extreme and mostly consist of a few new tags and making hard lines about how certain tags should be formatted and named. I'd try it first. At worst, you might have to change some of the ...
written 9 days ago by jared.andrews07320
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Comment: C: How can I see the distribution of TFBS on specific enhancer in UCSC
... Do you want the distribution or just to know which are enriched for your enhancer regions? If it's the latter, you can try [AME](http://meme-suite.org/doc/ame.html), which is made for just that. ...
written 13 days ago by jared.andrews07320
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Comment: C: How can I see the distribution of TFBS on specific enhancer in UCSC
... Depends how many PWMs you want it to look for. If you use a full database, like all of the JASPAR CORE, it takes a pretty long time, but you can cut it down by breaking the genome up into chromosomes and using [GNU Parallel][1] to run it on them in parallel, then just concatenate the results. The re ...
written 13 days ago by jared.andrews07320
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Comment: C: bedops vcf2bed eats up all allocated memory
... Sounds like giving it 72G of RAM might work, Ram. ...Sorry, couldn't pass it up. Seriously though, the `vcf2bed` and `convert2bed` commands don't have a ton of options. Alex could probably give you a solution though, dude's a wizard. Alternatively, you could filter based on the variant type in th ...
written 14 days ago by jared.andrews07320

Latest awards to jared.andrews07

Scholar 29 days ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Autobiographer 4 months ago, has more than 80 characters in the information field of the user's profile.

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