Moderator: Chris Miller
Chris Miller ♦ 20k
- Reputation:
- 20,200
- Status:
- Trusted
- Location:
- Washington University in St. Louis, MO
- Website:
- http://chrismiller.sci...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day, 16 hours ago
- Joined:
- 8 years, 11 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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... Just a note to say that I'm collaborating with Allegra on several projects, and it's a great environment, with a lot of exciting research going on, especially in the single-cell cancer genomics space. ...
written 8 weeks ago by
Chris Miller ♦ 20k
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... You're going to have better luck getting useful answers if you a) show evidence that you've tried to research this problem yourself b) tell us what you've tried, and c) provide more details ...
written 9 weeks ago by
Chris Miller ♦ 20k
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... Highly suggest that you check out the [pVACtools](https://pvactools.readthedocs.io/en/latest/) suite, which utilizes some VEP plugins and custom parsing to extract exactly this information and format it nicely prior to doing binding affinity predictions. ...
written 10 weeks ago by
Chris Miller ♦ 20k
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... > To get SNPs specific to horn cancer, I have subtract Horn Normal vcf file from Horn Cancer vcf file using bedtools.
Don't do this. The assumptions that germline variant callers make about VAF distributions and such don't lend themselves well to calling cancer variants. You need to use a true s ...
written 10 weeks ago by
Chris Miller ♦ 20k
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Comment:
C: a question about fishplot
... I should mention that you can also dig into the drawing code if you really want to tweak things. If you come up with useful options, pull requests are welcome! ...
written 3 months ago by
Chris Miller ♦ 20k
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Answer:
A: a question about fishplot
... That has to do with the way that the splining function is generating curves to fit your points. Unfortunately, the goals of having perfectly smooth curves and conforming precisely to the values you enter are mutually exclusive (or at least quite difficult!) If you want a perfectly smooth one, you ca ...
written 3 months ago by
Chris Miller ♦ 20k
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... It looks like you have a sequence data that was aligned to a transcriptome, rather than a genome. If you want to use IGV, you will either need to a) create a new "genome" for IGV with one contig per gene (this is almost certainly not what you want) or b) align your RNAseq data to a genome, using s ...
written 3 months ago by
Chris Miller ♦ 20k
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... Some tumors have it, some don't. To the best of my knowledge, the GDC (https://portal.gdc.cancer.gov/) is currently the canonical source for TCGA data. ...
written 4 months ago by
Chris Miller ♦ 20k
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... This tool accepts a peak file, and looks for enriched motifs under those peaks:
http://homer.ucsd.edu/homer/ngs/peakMotifs.html ...
written 4 months ago by
Chris Miller ♦ 20k
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... Those are somatic mutations and are all called in the tumor samples relative to the normal. Germline mutations are protected with an additional level of restrictions, but are available, but almost certainly in VCF, not MAF format. ...
written 4 months ago by
Chris Miller ♦ 20k
Latest awards to Chris Miller
Epic Question
4 days ago,
created a question with more than 10,000 views.
For Bioinformatics "Cheat Sheet"
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9 weeks ago,
created a comment with at least 3 up-votes.
For C: All Possible Substitutions In The Human Reference Genome
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: How to aggregate multiple copy number variation profiles or select the best one
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Scholar
3 months ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Good Answer
3 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
3 months ago,
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For Long-Term Hosting For Large Annotation Files?
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4 months ago,
asked a question with at least 3 up-votes.
For Importing A Large Number Of References From Text
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4 months ago,
asked a question that was upvoted at least 5 times.
For Importing A Large Number Of References From Text
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created a post with more than 5 votes.
For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer
4 months ago,
created an answer that was upvoted at least 5 times.
For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Scholar
5 months ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Appreciated
5 months ago,
created a post with more than 5 votes.
For C: Should Biostar Be Switched Over To The Stackexchange Network?
Scholar
7 months ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Efficiently storing methylation data from BS-sequencing
Scholar
9 months ago,
created an answer that has been accepted.
For A: Spliting a dataframe based in a chromosome
Commentator
10 months ago,
created a comment with at least 3 up-votes.
For C: All Possible Substitutions In The Human Reference Genome
Appreciated
12 months ago,
created a post with more than 5 votes.
For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer
12 months ago,
created an answer that was upvoted at least 5 times.
For A: Should I Remove The Unmapped Reads From My Bam ?
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