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Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
Reputation:
17,370
Status:
Trusted
Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Twitter:
jermdemo
Scholar ID:
Google Scholar Page
Last seen:
2 days, 2 hours ago
Joined:
8 years, 5 months ago
Email:
l******@gmail.com

I am a bioinformatics software developer known mostly for my posts on big-ass servers, damn microarray papers, and the reproducible research guilt trip, as well as my review of pipeline frameworks. I have worked in virology, crop genomics, and on various pediatric diseases as a programmer, analyst, and architect. I'm currently a PhD student at Drexel.

Posts by Jeremy Leipzig

<prev • 815 results • page 1 of 82 • next >
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NCBI esearch for cited papers with public SRA data
... I'm interested in finding all recent (>=2017/01/01) papers with at least 5 citations and open associated SRA data in Entrez. Can someone provide an automated strategy for this? ...
ncbi sra esearch entrez written 24 days ago by Jeremy Leipzig ♦ 17k
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Answer: A: How do variant callers get genotype info?
... Usually the caller has no idea which chromosome homolog a variant is on. It can just see variants that are in the same read or read pair (unlikely for short reads) or it can try to infer which variants are on the same chromosome homolog (phased) using read-backed phasing (as part of the read assembl ...
written 9 weeks ago by Jeremy Leipzig ♦ 17k
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Comment: C: How to take in consideration UMI in WES pipeline?
... TIL: UMIs are "unique molecular identifiers", more widely known as barcodes ...
written 11 weeks ago by Jeremy Leipzig ♦ 17k
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Comment: C: TMB Tumor Mutation Burden
... I think they sequence to ridiculously high median depth (500X) so they might have started to saturate by then? That having been said it's a crude metric for 2018 to say the least. I'm surprised it even has a name. ...
written 12 weeks ago by Jeremy Leipzig ♦ 17k
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Comment: C: Workflows! Where is the code?
... That sounds about right. I'm using the term "configuration" to describe configuration-based (using a specification markup language) rather than convention-based DSLs: https://academic.oup.com/bib/article/18/3/530/2562749 ...
written 12 weeks ago by Jeremy Leipzig ♦ 17k
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Answer: A: Workflows! Where is the code?
... CWL and WDL are specifications for configuration-based pipeline frameworks. These don't allow a lot of inline code, unlike domain specific languages. ...
written 3 months ago by Jeremy Leipzig ♦ 17k
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Comment: C: R or python, which one do you prefer in analysing scRNAseq datasets?
... > "my laptop" who told you that was an acceptable platform? ...
written 3 months ago by Jeremy Leipzig ♦ 17k
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Answer: A: Difference between FC and LogFC
... "fold change" is a bad metric and also the term itself can be ambiguous when speaking to different people, as evidenced by the confused entry in wikipedia https://en.wikipedia.org/wiki/Fold_change "log2 fold change" is symmetric and unambiguous ...
written 3 months ago by Jeremy Leipzig ♦ 17k
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Comment: C: New to bioinformatics.....
... "What my team has developed under my expert leadership is a comprehensive solution for data-driven predictive personalized medicine and cost savings. Big Data. IoT." ...
written 4 months ago by Jeremy Leipzig ♦ 17k
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Comment: C: New to bioinformatics.....
... Nonsense, this guy is executive material. He'll be my boss someday. ...
written 4 months ago by Jeremy Leipzig ♦ 17k

Latest awards to Jeremy Leipzig

Commentator 9 days ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 20 days ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Student 23 days ago, asked a question with at least 3 up-votes. For What are the best examples of sample naming conventions?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Epic Question 11 weeks ago, created a question with more than 10,000 views. For Where Can I Get The Asperasoft Command Line Client Ascp
Popular Question 3 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Appreciated 3 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 4 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Appreciated 4 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 4 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Scholar 6 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Great Question 10 months ago, created a question with more than 5,000 views. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How Much Does It Cost To Align A Flowcell In The Cloud?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Makefile-Driven Workflows And Bioconductor Objects
Popular Question 11 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
Popular Question 13 months ago, created a question with more than 1,000 views. For Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent?
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