Moderator: Chris Miller
Chris Miller ♦ 21k
- Reputation:
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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
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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.
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... 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 Miller ♦ 21k
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... 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 Miller ♦ 21k
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... 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 Miller ♦ 21k
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... 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 Miller ♦ 21k
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... 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 Miller ♦ 21k
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... 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 Miller ♦ 21k
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... 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 Miller ♦ 21k
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... 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 ...
written 13 months ago by
Chris Miller ♦ 21k
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... 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 Miller ♦ 21k
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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 Miller ♦ 21k
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For C: All Possible Substitutions In The Human Reference Genome
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For C: Should Biostar Be Switched Over To The Stackexchange Network?
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For A: Tool To Generate Proportional Venn Diagrams?
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For A: Spliting a dataframe based in a chromosome
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For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
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