Moderator: Jeremy Leipzig

gravatar for Jeremy Leipzig
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19,150
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Location:
Philadelphia, PA
Website:
http://jermdemo.blogsp...
Twitter:
jermdemo
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Google Scholar Page
Last seen:
13 hours ago
Joined:
10 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: Paper: Ten simple rules for biologists initiating a collaboration with computer
... that is the essence of the robustness survey I am conducting https://www.biostars.org/p/466772/ ...
written 3 days ago by Jeremy Leipzig19k
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Answer: A: Paper: Ten simple rules for biologists initiating a collaboration with computer
... It's ok. Would have preferred that she explicitly discuss "Metadata for biologists" and "data cleaning" instead of dancing around the subject. I think she needed to establish data, code, pipelines, notebooks, papers in a more rigid fashion for biologists to understand how to structure things for a c ...
written 3 days ago by Jeremy Leipzig19k
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Answer: A: Publicly Available RNA-Seq Datasets from Human Heart
... https://jhubiostatistics.shinyapps.io/recount/ I see at least 16 studies with cardiac tissue ...
written 5 days ago by Jeremy Leipzig19k
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News: Paid opportunity: need microbiome experts for a survey and test of robustness
... I am looking for participants to complete a survey and programming task to gauge the effectiveness of tests of robustness for peer review. The survey consists of several questions about reproducible research, open data, and peer review. The programmatic task involves reading a manuscript, studying t ...
survey news written 14 days ago by Jeremy Leipzig19k
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Answer: A: merging overlaping ranges with GenomicRanges
... > myranges<-GRanges(seqnames=c("chr1","chr1","chr1","chr1"),ranges=IRanges(start=c(382055,381772,262655,262580),end=c(382118,381832,262913,262913))) > reduce(myranges) GRanges object with 3 ranges and 0 metadata columns: seqnames ranges strand ...
written 25 days ago by Jeremy Leipzig19k
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Comment: C: How to submit the stop codon free complete mitochondrial genome sequence in Genb
... the reading frame is mooved over is off by 1 or maybe 2 nucleotides, so you are seeing a stop codon instead of the correct amino acid. Make sure you are using the correct coordinates for Bos frontalis by aligning your sequence with one of the ones here https://www.ncbi.nlm.nih.gov/nuccore/?term=Bos+ ...
written 4 weeks ago by Jeremy Leipzig19k
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Comment: C: How to submit the stop codon free complete mitochondrial genome sequence in Genb
... this would make sense if you sequenced a Bos Indicus instead of a Bos Taurus? https://www.ncbi.nlm.nih.gov/nucleotide/NC_005971.1 ...
written 4 weeks ago by Jeremy Leipzig19k
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Comment: C: How to submit the stop codon free complete mitochondrial genome sequence in Genb
... oh this is udderly problematic. if every gene is generating this maybe you are facing a 1-off frameshift error? ...
written 4 weeks ago by Jeremy Leipzig19k
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Comment: C: How to submit the stop codon free complete mitochondrial genome sequence in Genb
... ok did you use these coordinates? https://www.ncbi.nlm.nih.gov/nuccore/LC576822.1 ...
written 4 weeks ago by Jeremy Leipzig19k
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Comment: C: How to submit the stop codon free complete mitochondrial genome sequence in Genb
... which mammal is this you've sequenced? are you borrowing the start-stop coordinates from human mtdna? ...
written 4 weeks ago by Jeremy Leipzig19k

Latest awards to Jeremy Leipzig

Scholar 13 days ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Appreciated 13 days ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Did dbSNP not get the memo about hg38 chromosome names?
Great Question 6 weeks ago, created a question with more than 5,000 views. For Are There Websites Which Allow Users To Post Comments On Peer-Reviewed Articles?
Scholar 6 weeks ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Did dbSNP not get the memo about hg38 chromosome names?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 8 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Appreciated 8 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Popular Question 10 months ago, created a question with more than 1,000 views. For Pegasus Vs Taverna
Popular Question 11 months ago, created a question with more than 1,000 views. For Pegasus Vs Taverna
Great Question 12 months ago, created a question with more than 5,000 views. For Which C++ Libraries Are Best For Dealing With Fastq Files?
Scholar 13 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Appreciated 13 months ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?
Scholar 13 months ago, created an answer that has been accepted. For A: Retrieve mutation position and ID for a mutation in hgvs format
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What Coverage For Genome Re-Sequencing By Illumina ?

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