Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller21k
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20,970
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Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
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Google Scholar Page
Last seen:
2 days, 10 hours ago
Joined:
10 years, 1 month ago
Email:
c***********@gmail.com

I work in the Division of Oncology and McDonnell Genome Institute at Washington University in St. Louis, where I develop and apply computational tools to give us insight into the origins and progression of cancer.

Posts by Chris Miller

<prev • 1,101 results • page 2 of 111 • next >
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Answer: A: HGVS format to VCF from portal.gdc.cancer.gov
... Those are essentially genomic coordinates, right? I think you could just parse out the extra crap then give it to VEP to create a valid VCF: https://m.ensembl.org/info/docs/tools/vep/vep_formats.html#default I've done similar things to get wacky formats into VCF ...
written 12 months ago by Chris Miller21k
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Answer: A: Saving 3D plot from rgl as a pdf
... This function is an example of using rgl to render a 3d plot and spin it, taking periodic snapshots and assembling them into a gif: https://github.com/genome/sciclone/blob/master/R/plots.R#L1171 It's been years since I wrote that, and the details are a bit fuzzy, but maybe it provides some useful ...
written 12 months ago by Chris Miller21k
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Comment: C: Middle author, but not first author projects. How would you approach this?
... Bosses can make your life hell in plenty of other ways... I know a person who did this without including or notifying the head of their lab and got dressed down pretty good for it, since the review covered things he learned/worked on while in lab. There's a whole separate discussion to be had abou ...
written 12 months ago by Chris Miller21k
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Comment: C: Middle author, but not first author projects. How would you approach this?
... Be very careful going this route. Working on things related to your field, even if "on your own time" is often not advisable politically, even if technically allowed. ...
written 12 months ago by Chris Miller21k
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Comment: C: Middle author, but not first author projects. How would you approach this?
... If you are working for someone who doesn't appreciate computational contributions, my suggestion would be to find a new boss. ...
written 12 months ago by Chris Miller21k
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Comment: C: CNVkit: Choice of Bin Size and CNV Calling
... CopyCat should work fine with newer R versions, as far as I know, and has a single-sample mode ...
written 13 months ago by Chris Miller21k
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Answer: A: CNVkit: Choice of Bin Size and CNV Calling
... It's a tradeoff. Larger bin sizes reduce noise, smaller bin sizes increase sensitivity. This figure (panels C and D) may offer some clarity on that point, as does some of the text immediately below https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016327#pone-0016327-g001 In gene ...
written 13 months ago by Chris Miller21k
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Job: Bioinformatics Developer/Analyst - Washington University in St. Louis
... Our cancer genomics team is expanding by adding additional analysts and developers. You'll join a well-established group of computationally-savvy researchers working on cutting edge questions in the field. This group, under the Genomics of AML Program Project Grant, sequenced the first human cancer ...
job wustl written 13 months ago by Chris Miller21k
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Comment: C: Visualize VarScan2 Copy Number Aberrations in IGV
... The primary issue is that most copy number events are of size megabase or more. IGV works best on the base-to-kilobase scale. You certainly can make bed-like tracks that show your CN event, but it's probably not going to be the most helpful view.. ...
written 14 months ago by Chris Miller21k
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Answer: A: Reproducing this picture
... GenVisR is a good R package for this, as is ProteinPaint from St Jude: https://pecan.stjude.cloud/proteinpaint ...
written 14 months ago by Chris Miller21k

Latest awards to Chris Miller

Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 3 months ago, created an answer that has been accepted. For A: Modifying A Gene Sequence With Personal Snps?
Scholar 3 months ago, created an answer that has been accepted. For A: How to aggregate multiple copy number variation profiles or select the best one
Scholar 3 months ago, created an answer that has been accepted. For A: How to aggregate multiple copy number variation profiles or select the best one
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 4 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Scholar 5 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Tool To Generate Proportional Venn Diagrams?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Great Question 10 months ago, created a question with more than 5,000 views. For Biomart Very Slow
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 10 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack

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