Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
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Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Twitter:
jermdemo
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Google Scholar Page
Last seen:
3 hours ago
Joined:
7 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

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Comment: C: How do you run a BWA alignnment command in R?
... ...or why not use one of the many fine pipeline frameworks actually designed for this? ...
written 29 days ago by Jeremy Leipzig17k
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Comment: C: Goseq: Pwf: Error In If (Hi <= Low) { : Missing Value Where True/False Needed
... Show us what `genes` looks like after your faulty code above. ...
written 29 days ago by Jeremy Leipzig17k
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Comment: C: Goseq: Pwf: Error In If (Hi <= Low) { : Missing Value Where True/False Needed
... that R is gibberish. What do you think the gene vector should look like? ...
written 4 weeks ago by Jeremy Leipzig17k
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Comment: C: Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
... for general editing I have been using Cloud9 https://c9.io, which is definitely not free if you need privacy but is definitely worth every penny ...
written 6 weeks ago by Jeremy Leipzig17k
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Comment: C: CWL rerunning completed output
... though I've never tested CWL with either of these tools - both Toil https://toil.readthedocs.io/en/3.10.0/running/cwl.html and Nextflow https://github.com/nextflow-io/cwl2nxf offer some support for CWL and are reentrant ...
written 6 weeks ago by Jeremy Leipzig17k
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Comment: C: RUM aligner - perl precedence error
... i don't think even the RUM people use RUM anymore ...
written 6 weeks ago by Jeremy Leipzig17k
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Comment: C: CWL rerunning completed output
... yes reentrancy is one of those things the make crowd takes for granted but the workbench people find especially challenging to implement ...
written 6 weeks ago by Jeremy Leipzig17k
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Comment: C: How to handle metadata in bioinformatics pipelines?
... yes nice support for ontologies to define input/output formats in CWL https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/master/tools/fastq_to_fasta.cwl cwlVersion: v1.0 class: CommandLineTool hints: - class: SoftwareRequirement packages: biopytho ...
written 11 weeks ago by Jeremy Leipzig17k
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Answer: A: Rare Variant Association Tests and ExAC Data Set
... ![http://i.imgur.com/IAYtE2il.png][1] [1]: http://i.imgur.com/IAYtE2il.png ...
written 4 months ago by Jeremy Leipzig17k
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Comment: C: is seqanswers.com down?
... Hello mjp! We believe that this post does not fit the main topic of this site. off-topic For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll be happy to ...
written 4 months ago by Jeremy Leipzig17k

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Great Question 18 days 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 5 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?
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Makefile-Driven Workflows And Bioconductor Objects
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?
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?
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?
Prophet 4 months ago, created a post with more than 20 followers. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
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Good Question 4 months ago, asked a question that was upvoted at least 5 times. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Teacher 5 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?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Is Biostar Killing The Bioinformatics Core?
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 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?
Scholar 5 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Appreciated 5 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Is Biostar Killing The Bioinformatics Core?
Great Question 6 months ago, created a question with more than 5,000 views. For Which C++ Libraries Are Best For Dealing With Fastq Files?
Epic Question 6 months ago, created a question with more than 10,000 views. For Where Can I Get The Asperasoft Command Line Client Ascp
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?
Great Question 7 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?
Great Question 8 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?
Good Answer 8 months 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 9 months ago, created a question with more than 1,000 views. For Is There A Convention For Representing Indels In Diploid Genome Sequences?
Popular Question 9 months ago, created a question with more than 1,000 views. For Is There A Convention For Representing Indels In Diploid Genome Sequences?
Student 10 months ago, asked a question with at least 3 up-votes. For Why Do Genbank And Refseq Have Different Coordinates For Mitochondrial Features?

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