User: eric.kern13

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eric.kern1390
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Posts by eric.kern13

<prev • 35 results • page 1 of 4 • next >
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Answer: A: Overdispersion for single cell RNA seq experiments
... What have you tried so far? One sensible solution might be to try: - whatever you would try if you didn't have to worry about low counts; maybe K-means - some out-of-the-box method such as PAGODA. http://hms-dbmi.github.io/scde/pagoda.html If those don't get you to where you need to be, then where ...
written 3 months ago by eric.kern1390
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Comment: C: Question about dbSNP rs #s
... Do you know of an easy way to update rsid's that have been retired? ...
written 6 months ago by eric.kern1390
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Comment: C: Duplicated Reads In Rna-Seq Experiment
... (I would like to hear the answer to this as well.) ...
written 9 months ago by eric.kern1390
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Comment: C: Should We Remove Duplicated Reads In Rna-Seq ?
... 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 9 months ago by eric.kern1390
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What happens during seed stitching when STAR initially gets the wrong MMP?
... 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 ...
star rna-seq written 11 months ago by eric.kern1390 • updated 11 months ago by Santosh Anand3.5k
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Comment: C: Retrieve all genes under a mammalian phenotype ontology term
... Works like a charm. Thank you very much! ...
written 12 months ago by eric.kern1390
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Comment: C: Retrieve all genes under a mammalian phenotype ontology term
... I tried to; it didn't work. I'll try again. ...
written 12 months ago by eric.kern1390
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Retrieve all genes under a mammalian phenotype ontology term
... 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 ...
R biomart go mammalian phenotype ontology written 12 months ago by eric.kern1390 • updated 12 months ago by Mike Smith640
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Comment: C: cell surface receptor genes
... Thanks for this list of resources! ...
written 19 months ago by eric.kern1390
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Answer: A: Interpreting ANNOVAR allele frequency output
... 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 19 months ago by eric.kern1390

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For +/- strand conventions for probe sequences
Popular Question 3 months ago, created a question with more than 1,000 views. For Pysam cannot find index
Supporter 6 months ago, voted at least 25 times.
Popular Question 19 months ago, created a question with more than 1,000 views. For Pysam cannot find index
Scholar 19 months ago, created an answer that has been accepted. For A: Looking for experience
Scholar 2.8 years ago, created an answer that has been accepted. For A: Looking for experience
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Looking for experience

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