User: jared.andrews07

gravatar for jared.andrews07
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640
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Location:
Washington University in St. Louis
Website:
https://github.com/j-a...
Last seen:
1 day, 18 hours ago
Joined:
8 months 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 • 100 results • page 1 of 10 • next >
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Answer: A: RNA-SEQ: Gene ontology terms is vague
... 1.) How are you doing your enrichment? This will help us better interpret Q2 and Q3 as well. I like tools like [enrichR][1], [DAVID][2], etc, that make pathway enrichment very straightforward and usually have pretty good default settings in terms of their thresholds. And lots of GO terms *are* vague ...
written 1 day ago by jared.andrews07640
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Comment: C: RNA-SEQ: Pathway analyses correlation to pathway activity
... To some extent, sure, but there are *plenty* of proteins that aren't expressed at any meaningful level. If many copies of a protein are necessary for measurable function, a few copies aren't going to yield any functional difference from a complete knockout, regardless of any post-translational modif ...
written 1 day ago by jared.andrews07640
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Answer: A: RNA-SEQ: Pathway analyses correlation to pathway activity
... While phosphorylation is certainly a factor for certain pathways, it doesn't play a part if said proteins are not expressed. This is particularly true for pathway enrichment, given that it makes sense that genes involved in the same biological processes would be transcriptionally co-regulated. Add ...
written 1 day ago by jared.andrews07640
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Answer: A: How to get descriptions for rs* SNP identifiers?
... You can use the [ENSEMBL RESTful API][1] in basically any language you'd want. It will return basic info and population frequencies. The [Variant Effect Predictor][2] may also be worth your time. I don't think these services will really help though, since blood type is mostly determined by only a ha ...
written 1 day ago by jared.andrews07640
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Comment: C: Knowledge from Gene
... Do you mean mode of inheritance? And which characteristics? For function, you can run the gene ID through uniprot to get a summary of the function. It's the best way to get generalized functions that I've found. [This post][1] should should probably get you started, but the uniprot API site will of ...
written 2 days ago by jared.andrews07640
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Comment: C: Knowledge from Gene
... What info is it missing that you'd want? ...
written 2 days ago by jared.andrews07640
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Answer: A: Are there any human genome variant callers and BAM indexing and sorting tools to
... Wiping Windows or converting fully to linux isn't necessary. You *can* easily get the best of both worlds - just use the [Linux subsystem for Windows][1]. Way easier than dealing with VMs or cygwin and can utilize all of your computer's resources rather than dealing with a gimped linux VM. I've neve ...
written 3 days ago by jared.andrews07640
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Answer: A: Knowledge from Gene
... [MyGene][1] has a pretty good and easy to use python API that yields tons of stuff - database IDs, function, etc. You can iterate through your gene names easily enough in Python to get all the info you'd want for each gene. They also let you try their [API online][2], so you can try that to see if t ...
written 3 days ago by jared.andrews07640
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Comment: C: Understanding the VCF data from my variant calling
... If you're just looking for variations in DNA, my first suggestion should work for you. Get the positions of your exons from your reference genome and intersect with them to pull out variants that lie within the exons from your VCF file. If you're looking for those that actually alter protein sequen ...
written 6 days ago by jared.andrews07640
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Answer: A: Understanding the VCF data from my variant calling
... Really need more information to properly answer this - are you just looking at variance or for deleterious changes? Regardless, you can filter your VCF file to pull out the variants for your region of interest quite easily with `bedtools intersect`. Additionally, you can annotate your VCF file wit ...
written 9 days ago by jared.andrews07640

Latest awards to jared.andrews07

Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 12 weeks ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 4 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
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