User: eric.kern13
eric.kern13 • 90
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Posts by eric.kern13
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... (I would like to hear the answer to this as well.) ...
written 7 weeks ago by
eric.kern13 • 90
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... This is an interesting comment and I'd like to understand it better. Are you using the word "regularization" in the statistical sense, for example as in "Tikhonov regularization"? If so, can you describe the statistical methods you have in mind? Also, how do you know that there are more duplicates p ...
written 7 weeks ago by
eric.kern13 • 90
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... Suppose I have the following read:
AAGGAAGGAAGGAAGGACTTCCTT
I want to align it to one of these two reference sequences:
AAGGAAGGAAGGAAGGACAAGGAA
AAGGAAGGAAGGAAGGCCTTCCTT
Clearly, the second reference sequence is where the read belongs: there's only one mismatch. The maximum mappable ...
written 3 months ago by
eric.kern13 • 90
• updated
3 months ago by
Santosh Anand • 2.9k
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... Works like a charm. Thank you very much! ...
written 4 months ago by
eric.kern13 • 90
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... I tried to; it didn't work. I'll try again. ...
written 4 months ago by
eric.kern13 • 90
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... I want to retrieve all genes corresponding to a given mammalian phenotype ontology term (for example, MP:0005375), preferably within R. Are there tools to do this? Can I do it within BioMart? Or is the best bet to build something around the APIs [here][1] or [here][2]?
Related: [similar question fo ...
written 4 months ago by
eric.kern13 • 90
• updated
4 months ago by
Mike Smith • 250
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Comment:
C: cell surface receptor genes
... Thanks for this list of resources! ...
written 11 months ago by
eric.kern13 • 90
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... Below, I quote a response from Kai Wang, ANNOVAR creator/maintainer:
> you should just use table_annovar.pl to print out allele frequency for
> all variants in your input. The word "minor allele frequency" cannot
> be defined well, because rare allele in one population will be common
> ...
written 11 months ago by
eric.kern13 • 90
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... Hi Biostars,
I'm using ANNOVAR to annotate some WGS data. I want to pare down the list until I am left with variants of very low frequency. I've got ANNOVAR working, but I'd appreciate your help interpreting its output. Here's what I did.
To split out the rare variants, I issued this command (or r ...
written 11 months ago by
eric.kern13 • 90
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... How many rows of data do you have? Linear models such as ANOVA rely heavily on independence of errors and constant variability, but with enough data, normality is not as crucial. ...
written 17 months ago by
eric.kern13 • 90
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