Moderator: brentp

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brentp22k
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Salt Lake City, UT
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https://github.com/brentp
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2 months, 1 week ago
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7 years, 2 months ago
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Working on bionformatics at the Quinlan Lab at the University of Utah.

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Posts by brentp

<prev • 938 results • page 1 of 94 • next >
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Answer: A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
... Certainly the ExAC paper: http://www.nature.com/nature/journal/v536/n7616/full/nature19057.html must be one of the top. published in August and cited > 200 times already. It's a game-changer for rare disease. ...
written 4 months ago by brentp22k
1
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Answer: A: How relevant, valuable, and important is Information Visualization nowadays in B
... If you can visualize data well, that means that you have the programming skills to parse and analyze the data. It means that you have enough of an understanding of the biology of the problem to know what visualizations and manipulations are useful. So, yes, there is a market for that. ...
written 6 months ago by brentp22k
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3
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3
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Answer: A: Principal Component Analysis using SNP data ste
... If your data is in VCF format, you can do this with peddy: https://github.com/brentp/peddy The command would look like: python -m peddy -p 4 --plot --prefix my.out $vcf $ped this will do a PCA with your samples projected onto those from thousand genomes and ancestry predicted according to tho ...
written 6 months ago by brentp22k
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Comment: C: Help with understanding CNVkit output
... so is it safe to assume that if the log2 < 0 it's a deletion, otherwise a dup? ...
written 10 months ago by brentp22k
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Answer: A: What is the reason for most software errors in Bioinformatics according to you?
... The simple reason that software has bugs (that result in errors) is that **writing software is hard**. Let's take a simple example and say you want to write some software to determine if a genetic variant meets an **autosomal recessive inheritance pattern**. This is **easy**, right!? Just find sit ...
written 14 months ago by brentp22k
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Comment: C: Black color reads in IGV: bwa-meth
... good to know ...
written 22 months ago by brentp22k
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Tool: vcfanno quickly annotate a vcf with other VCFs, BEDs, BAMs
... We have been developing vcfanno for some time now as a tool to quickly and easily annotate (put stuff in the info field) of a VCF. It is very fast, and binaries are provided for all major systems for both 32 and 64bit. There is help in the README, for introduction, but here we'll briefly cover the ...
vcf annotation tool written 23 months ago by brentp22k
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Comment: C: The new era of bioinformatics: simple and fast tools, fewer and more informative
... on the other hand, even small labs are doing dozens of whole genomes, requiring more infrastructure and analysts who are more than technicians.   ...
written 2.0 years ago by brentp22k
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Answer: A: sam/bam file handling -> new tools?
... you should also use vt normalize on your BAM files to left-align and trim. See this paper: http://bioinformatics.oxfordjournals.org/content/early/2015/02/19/bioinformatics.btv112.abstract for the difference it can make. ...
written 2.2 years ago by brentp22k
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Comment: C: When should you use SVA vs. ComBat?
... In short: If you know a covariate that drives the batch effect, use ComBat. If you don't use SVA. ...
written 2.2 years ago by brentp22k

Latest awards to brentp

Prophet 3 months ago, created a post with more than 20 followers. For What Are Numbers Every Bioinformatician Should Know?
Epic Question 4 months ago, created a question with more than 10,000 views. For Good Gwas Papers / Resources
Scholar 4 months ago, created an answer that has been accepted. For A: Using Rle (Relative Log Expression) Mean Values Of Microarray Data To Adjust For
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Correct Way To Parse A Fasta File In Python
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Global Pairwise Alignment For Long Sequence Throws Error In Python!!
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Global Pairwise Alignment For Long Sequence Throws Error In Python!!
Popular Question 5 months ago, created a question with more than 1,000 views. For Very Bad Things
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Correct Way To Parse A Fasta File In Python
Popular Question 7 months ago, created a question with more than 1,000 views. For Very Bad Things
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Doesn'T It Make Sense To Reduce Multiple Testing By Being More Selective With Ge
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Doesn'T It Make Sense To Reduce Multiple Testing By Being More Selective With Ge
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Global Pairwise Alignment For Long Sequence Throws Error In Python!!
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Global Pairwise Alignment For Long Sequence Throws Error In Python!!
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: How To Find Out Whether There Is A Statistical Difference Between Two Sets Of St
Popular Question 11 months ago, created a question with more than 1,000 views. For When Reviewing A Software Paper, Do You Talk About The Code Quality?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: I Am Preparing A Course On Ngs: Any Suggestion ?
Appreciated 11 months ago, created a post with more than 5 votes. For A: How To Generate Mutations In Sequences Of A Fasta File?
Appreciated 12 months ago, created a post with more than 5 votes. For A: Obtaining Exon Lengths:
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Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Looking Review Paper About P-Value, Adjusted P-Value And Multiple Test In Bioinf
Appreciated 13 months ago, created a post with more than 5 votes. For What Are Numbers Every Bioinformatician Should Know?
Appreciated 13 months ago, created a post with more than 5 votes. For What Are Numbers Every Bioinformatician Should Know?

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