User: robertobfisher

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Posts by robertobfisher

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Comment: C: gene enrichment analysis
... Ah, you're right. What I was thinking would be the chance of nature making those 50 balls red in the first place, what you say makes more sense. ...
written 2.3 years ago by robertobfisher30
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Comment: C: How to match genes of one file to another but in multiple columns
... s here should be a data structure that resembles a mathematical set (all elements unique). In Python, you can do `s = set()` to create an empty set and add elements with `s.add(g1)` and `s.add(g2)`. ...
written 2.3 years ago by robertobfisher30
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Comment: C: How to match genes of one file to another but in multiple columns
... Unfortunately I don't know many terminal commands so I wrote pseudocode instead. Hopefully you can convert it to a language you're familiar with. ...
written 2.3 years ago by robertobfisher30
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Comment: C: Taxonomic trait database?
... Most of these seem too focused on a particular group, but looking through `traits` I found EOL's TraitBank, which was what I wanted. Thanks! Strangely enough my search engine returned nothing useful for the same query. ...
written 2.3 years ago by robertobfisher30
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p-value for mutation calls from multiple reads
... Suppose I have sequenced a haploid genome. There is a position where I suspect I have a point mutation. I have `n` reads covering this position, with each read "voting" either A, T, C or G as its nucleotide call. The winner of the vote, in this case, is some nucleotide which is different than the re ...
snp written 2.3 years ago by robertobfisher30 • updated 2.2 years ago by Biostar ♦♦ 20
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Comment: C: gene enrichment analysis
... Wouldn't it be "chance that 28 genes would come from the 15k if the 50 were selected at random from the 20k"? ...
written 2.3 years ago by robertobfisher30
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Answer: A: How to match genes of one file to another but in multiple columns
... You could write a short script in a language like Python. Pseudocode: f1 = archoloro.txt f2 = ArabidopsisParalogue.txt s = construct set from f1 t = empty set for each line in f2 g1, g2 = split line at "\t" if g1 and g2 in s add g1, g2 to s If yo ...
written 2.3 years ago by robertobfisher30
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Taxonomic trait database?
... Is there a large database of phenotypic traits of various species? Probably most will focus on morphology, but behavior, diet, habitat would also be interesting. I am looking for as much variety as possible (mammals, birds, reptiles, fish, worms, bacteria, plants, fungi), and a good amount (ideally ...
database taxonomy written 2.3 years ago by robertobfisher30 • updated 2.3 years ago by h.mon30k

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