Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller21k
Reputation:
21,110
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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, 6 hours ago
Joined:
10 years, 5 months 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 • 1,106 results • page 2 of 111 • next >
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Answer: A: Tool to separate human and mouse rna seq reads
... We're testing out [XenoSplit](https://github.com/goknurginer/XenoSplit) right now and it seems to work fairly well. I've also used [NGS-disambiguate](https://github.com/AstraZeneca-NGS/disambiguate) in the past with success. ...
written 13 months ago by Chris Miller21k
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Job: Bioinformatics Programmer - Washington University in St. Louis
... We currently have an opening for a Bioinformatics Programmer in our cancer genomics group at Washington University in St. Louis. It's a great place to work, a fantastic place to do science, and a great opportunity for a talented coder to learn bioinformatics. Apply through the WUSTL jobs website at ...
analyst developer job genomics cancer written 13 months ago by Chris Miller21k
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Answer: A: Free for academic use only licenses (If you want to sell your software please ju
... Appreciate the perspective! I've navigated this from the academic side before, and it's tough. We all know that academic software has a reputation for being poorly engineered, and unsupported approximately 5 minutes after it's published. That's because it's _really_ hard to get grant funding for st ...
written 15 months ago by Chris Miller21k
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Comment: C: Bin chromosome every 1kb and get average value
... Even though Pierre has created a strange little masterpiece up there, I think this is going to be the best answer for most people :) ...
written 15 months ago by Chris Miller21k
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Comment: C: HGVS format to VCF from portal.gdc.cancer.gov
... If this works for you, great, but IIRC, that's not valid VCF format, because of the missing "anchor bases" for ins and del. (e.g. G/- should be CG/C) A lot of tools will get angry about that. VEP will fill those in with the missing ref bases, if you do end up needing them. ...
written 16 months ago by Chris Miller21k
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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 16 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 16 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 16 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 16 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 16 months ago by Chris Miller21k

Latest awards to Chris Miller

Scholar 10 weeks ago, created an answer that has been accepted. For A: How to aggregate multiple copy number variation profiles or select the best one
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Popular Question 6 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 7 months ago, created an answer that has been accepted. For A: Modifying A Gene Sequence With Personal Snps?
Scholar 7 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 7 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 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 8 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Scholar 9 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Tool To Generate Proportional Venn Diagrams?
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 12 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 12 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Great Question 14 months ago, created a question with more than 5,000 views. For Biomart Very Slow
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 14 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack

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