Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
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Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Twitter:
jermdemo
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Last seen:
6 hours ago
Joined:
8 years, 7 months ago
Email:
l******@gmail.com

I am a bioinformatics software developer known mostly for my posts on big-ass serversdamn 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 • 822 results • page 1 of 83 • next >
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Job: Bioinformatics Data Scientist and Postdoctoral Fellow - Xing lab @ CHOP
... Dr. Yi Xing’s lab (https://xinglab.org/) at the Children’s Hospital of Philadelphia (CHOP) and the University of Pennsylvania (Penn) has multiple openings for Bioinformatics Data Scientist or Postdoctoral Fellow. Our lab is broadly interested in computational biology and genomics of RNA processing a ...
splicing job rna-seq written 1 day ago by Jeremy Leipzig17k
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Answer: A: Mean Length Of Fasta Sequences
... this is a nim solution import strutils var line: string seqCnt = 0 charCnt = 0 proc main()= for line in stdin.lines: if line.startsWith('>'): inc seqCnt else: charCnt += len(line) echo (charCnt/seqCnt) ma ...
written 15 days ago by Jeremy Leipzig17k
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mixed models with phylogenetic trees
... Is there a package that takes a phylogenetic tree and allows you to specify fixed and random effects by specifying a level of the tree, so everything above is random and everything below is fixed (or vice-versa)? So if you have a homologous SNP in some distant species and some phenotypic measure, y ...
mixed-models written 16 days ago by Jeremy Leipzig17k
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Comment: C: how to map a probeset to a reference?
... it is a custom array derived from some freeze of a genome ...
written 23 days ago by Jeremy Leipzig17k
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Comment: C: how to map a probeset to a reference?
... right this is a complete mystery, so I need a very sparse gappy aligner or something that can take a list of chromosomal coordinates and extract the sequences from every genome on earth ...
written 23 days ago by Jeremy Leipzig17k
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Comment: C: how to map a probeset to a reference?
... I only have the SNPs that the probes interrogate, not the actual probe sequences ...
written 23 days ago by Jeremy Leipzig17k
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how to map a probeset to a reference?
... Let's say you were given a microarray probeset, consisting of sparsely scattered SNPs of Allele A and B. If you didn't know from which genome or freeze it was derived, how would you find out? ...
microarray snp probeset written 23 days ago by Jeremy Leipzig17k
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Answer: A: Any suggestions for basic intro to submitting jobs to an HPC cluster?
... 1. Your estimates should be derived from empirical evidence. SGE has `qacct` which should tell you how much memory was consumed at peak for a completed process. 2. A memory-bound process can certainly be slowed by lack of memory, but it's more likely to just crash. Computers are great at managing li ...
written 7 weeks ago by Jeremy Leipzig17k
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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 12 weeks ago by Jeremy Leipzig17k
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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 4 months ago by Jeremy Leipzig17k

Latest awards to Jeremy Leipzig

Popular Question 5 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?
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 6 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?
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Good Answer 12 weeks 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 12 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?
Student 12 weeks ago, asked a question with at least 3 up-votes. For What are the best examples of sample naming conventions?
Teacher 3 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?
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?
Teacher 4 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?
Scholar 4 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Epic Question 4 months ago, created a question with more than 10,000 views. For Where Can I Get The Asperasoft Command Line Client Ascp
Popular Question 5 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 5 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Appreciated 5 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 6 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 6 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Big Ass Servers & Storage
Appreciated 6 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 7 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 8 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 8 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 10 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 12 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?

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