Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller21k
Reputation:
20,650
Status:
Trusted
Location:
Washington University in St. Louis, MO
Website:
http://chrismiller.sci...
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
9 years, 4 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 • 1,100 results • page 1 of 110 • next >
2
votes
1
answer
64
views
1
answers
Answer: A: Using Varscan without a matched normal
... Somatic calling is essentially just calling differences between two samples. If you use a tumor as your control and a metastasis as your case, then you'll call metastasis-specific mutations (but will miss any somatic mutations shared between the tumor and met). ...
written 6 days ago by Chris Miller21k
3
votes
1
answer
63
views
1
answers
Answer: A: How can I get this sorted by ascending order? (when the number and character is
... If you're using GNU sort, then "sort -V" will do what you want. In general, though, it's not necesary. The community has (somewhat) standardized on character sort order, which is what you have there. ...
written 7 days ago by Chris Miller21k
1
vote
5
answers
24k
views
5
answers
Comment: C: How Can I Know The Length Of Mapped Reads From Bam File?
... Sure - make it `samtools view -F 4 file.bam ...` if you want only mapped ...
written 7 days ago by Chris Miller21k
3
votes
3
answers
5.3k
views
3
answers
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 14 days ago by Chris Miller21k
0
votes
0
answers
382
views
0
answers
Job: Bioinformatics Developer/Analyst - Washington University in St. Louis
... We currently have an opening for a Bioinformatics Developer/Analyst 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 web ...
analyst developer job genomics cancer written 25 days ago by Chris Miller21k
3
votes
1
answer
267
views
1
answers
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 11 weeks ago by Chris Miller21k
0
votes
3
answers
1.4k
views
3
answers
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 12 weeks ago by Chris Miller21k
0
votes
3
answers
290
views
3
answers
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 3 months ago by Chris Miller21k
1
vote
3
answers
290
views
3
answers
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 3 months ago by Chris Miller21k
1
vote
3
answers
395
views
3
answers
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 3 months ago by Chris Miller21k

Latest awards to Chris Miller

Teacher 12 hours ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 6 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 6 days ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Great Question 6 weeks ago, created a question with more than 5,000 views. For Biomart Very Slow
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Scholar 4 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Popular Question 5 months ago, created a question with more than 1,000 views. For Cancer Genomics/Genomic Medicine - The Genome Institute at WUSTL
Epic Question 5 months ago, created a question with more than 10,000 views. For Bioinformatics "Cheat Sheet"
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Scholar 8 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 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Any Experiences/Solutions For Problems With The Last R Update?
Student 8 months ago, asked a question with at least 3 up-votes. For Long-Term Hosting For Large Annotation Files?
Student 9 months ago, asked a question with at least 3 up-votes. For Importing A Large Number Of References From Text

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1932 users visited in the last hour