Moderator: Chris Miller
Chris Miller ♦ 21k
- Reputation:
- 21,110
- Status:
- Trusted
- Location:
- Washington University in St. Louis, MO
- Website:
- http://chrismiller.sci...
- Scholar ID:
- 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.
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... 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 Miller ♦ 21k
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... 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 ...
written 13 months ago by
Chris Miller ♦ 21k
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... 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 Miller ♦ 21k
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... 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 Miller ♦ 21k
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... 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 Miller ♦ 21k
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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 16 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 16 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 16 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 16 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 16 months ago by
Chris Miller ♦ 21k
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
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
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
Scholar
12 months ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Scholar
12 months ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
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