Moderator: Jeremy Leipzig
Jeremy Leipzig ♦ 19k
- Reputation:
- 19,150
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- Location:
- Philadelphia, PA
- Website:
- http://jermdemo.blogsp...
- Twitter:
- jermdemo
- Scholar ID:
- 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 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
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... that is the essence of the robustness survey I am conducting https://www.biostars.org/p/466772/ ...
written 3 days ago by
Jeremy Leipzig ♦ 19k
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... 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 Leipzig ♦ 19k
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... https://jhubiostatistics.shinyapps.io/recount/
I see at least 16 studies with cardiac tissue ...
written 5 days ago by
Jeremy Leipzig ♦ 19k
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... 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 ...
written 14 days ago by
Jeremy Leipzig ♦ 19k
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... > 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 Leipzig ♦ 19k
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... 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 Leipzig ♦ 19k
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... 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 Leipzig ♦ 19k
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... 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 Leipzig ♦ 19k
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... ok did you use these coordinates? https://www.ncbi.nlm.nih.gov/nuccore/LC576822.1 ...
written 4 weeks ago by
Jeremy Leipzig ♦ 19k
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... which mammal is this you've sequenced? are you borrowing the start-stop coordinates from human mtdna? ...
written 4 weeks ago by
Jeremy Leipzig ♦ 19k
Latest awards to Jeremy Leipzig
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13 days ago,
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For A: Retrieve mutation position and ID for a mutation in hgvs format
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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
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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,
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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,
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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,
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For Pegasus Vs Taverna
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For Pegasus Vs Taverna
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For Which C++ Libraries Are Best For Dealing With Fastq Files?
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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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