Moderator: David W

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David W4.6k
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Posts by David W

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Comment: C: Watterson's estimator "theta"
... Maybe read this, then ask a more specific question if you are still unclear? https://en.wikipedia.org/wiki/Watterson_estimator ...
written 2.3 years ago by David W4.6k
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Answer: A: Quickly subsetting VCF while being memory efficient
... I don't know if it can be used in the particular case you are taking about, but genome query tools (https://github.com/ryanlayer/gqt) has been written specifically to handle very large genotype  files and with low memory footprint and speedy queries.  EDIT Some of gqt's tricks are specifically for ...
written 2.3 years ago by David W4.6k
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Comment: C: Quickly subsetting VCF while being memory efficient
... I recently ran a similar task to the OPs with the mask saved as BED files. First time I ran it'd forgotten to tabix the files: ~7hrs to run. Once I'd tabixed them ~ 1 minute :) ...
written 2.3 years ago by David W4.6k
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Answer: A: Parse the Xml response from Entrez Db=bioproject Using Biopython eFetch
... This seems to be a problem with the Bioproject database not having a DTD: http://lists.open-bio.org/pipermail/biopython/2015-May/015632.html That thread has a work-around, but you might also want to try the development version of Biopython (https://github.com/biopython/biopython)to see if the new ...
written 2.3 years ago by David W4.6k
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Answer: A: Bedtools: How to save output in Cygwin by creating a bed file?
... bedtools intersect -a a.bed -b b.bed > intersect_ab.bed The '>’ bit redirects the output into a (newly created/overwritten) file instead of printing to screen. Welcome to unix-like commands, once you 'get' this and piping you'll find you can do a lot from the command line :-) ...
written 2.3 years ago by David W4.6k
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Answer: A: Extract PMIDs from a gene or protein ID
... If you use the link EUtil with dbfrom="protein", db="pubmed" you'll get a list of pmids associated with that protein.  You can then use esummary or efetch on those pmids. ...
written 2.4 years ago by David W4.6k
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Comment: C: GTR always the best model of evolution
... Short "answer": to avoid overfitting: http://en.m.wikipedia.org/wiki/Overfitting ...
written 2.4 years ago by David W4.6k
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Answer: A: database that links EntrezGeneIDs and EnsemblIDs
... Biomart (linked to by Sean above) is pretty much your first port of call for all id-mapping problems.  In this case, ensembl also has a REST endpoint for gathering cross refs: http://rest.ensembl.org/xrefs/id/ENST00000288602?content-type=application/json;   ...
written 2.4 years ago by David W4.6k
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Answer: A: R programming question: insert alternately
... For anyone else interested in the different performance of these solutions, I did a crude comparison. The TLDR would be: the "grow a for loop" approach works for short vectors, but scales terribly. The rbind method, as unintuitive as it might be,  is the fastest of the lot   https://gist.github.c ...
written 2.4 years ago by David W4.6k
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Comment: C: R programming question: insert alternately
... This should get the job done, and for shorter vectors won't take too long. But be aware, starting an empty vector and growing it like this, though sensible in many languages, is usually very slow in r. I've not tested it, but as.character(rbind(a,b)) should work, and starting a vector of the final ...
written 2.4 years ago by David W4.6k

Latest awards to David W

Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: How Can I Compare Rates Of Evolution For Two Sets Of Genes?
Appreciated 18 months ago, created a post with more than 5 votes. For A: Unrooting Trees Help
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Unrooting Trees Help
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Unrooting Trees Help
Appreciated 23 months ago, created a post with more than 5 votes. For A: Unrooting Trees Help
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: How Can I Compare Rates Of Evolution For Two Sets Of Genes?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Unrooting Trees Help
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Looking For A Taxonomy With Species And Breeds
Scholar 2.3 years ago, created an answer that has been accepted. For A: Hierarchical tree based on phylogenetic profile matrix (presence/absence per spe
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Unrooting Trees Help
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Unrooting Trees Help
Scholar 2.4 years ago, created an answer that has been accepted. For A: Hierarchical tree based on phylogenetic profile matrix (presence/absence per spe
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Unrooting Trees Help
Scholar 2.4 years ago, created an answer that has been accepted. For A: Hierarchical tree based on phylogenetic profile matrix (presence/absence per spe
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Unrooting Trees Help
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Unrooting Trees Help
Scholar 2.5 years ago, created an answer that has been accepted. For A: Hierarchical tree based on phylogenetic profile matrix (presence/absence per spe
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Unrooting Trees Help
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Unrooting Trees Help
Scholar 2.5 years ago, created an answer that has been accepted. For A: Hierarchical tree based on phylogenetic profile matrix (presence/absence per spe
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Unrooting Trees Help
Scholar 2.6 years ago, created an answer that has been accepted. For A: Hierarchical tree based on phylogenetic profile matrix (presence/absence per spe
Scholar 2.6 years ago, created an answer that has been accepted. For A: Hierarchical tree based on phylogenetic profile matrix (presence/absence per spe
Scholar 2.6 years ago, created an answer that has been accepted. For A: Hierarchical tree based on phylogenetic profile matrix (presence/absence per spe

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