User: eric.kern13

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eric.kern13150
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3 months, 1 week ago
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Posts by eric.kern13

<prev • 39 results • page 1 of 4 • next >
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Comment: C: Using Seurat 3 Data for Pseudotime Analysis in Monocle 3
... jared.andrews07, could you explain how scanpy can directly convert Seurat objects? Your link may have changed but it currently points to a generic ScanPy docs page. ...
written 3 months ago by eric.kern13150
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Comment: C: Help setting up lncRNA-screen from github
... Did you ever get this working? I am interested to compare notes regarding the format of the resulting BED file. ...
written 13 months ago by eric.kern13150
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Comment: C: How To Write Data In A Granges Object To A Bed File.
... Your link currently gives this thread as the first hit. Profit indeed. ...
written 16 months ago by eric.kern13150
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Answer: A: Adapter/Linker/Primer Sequence Database?
... Using the ncbi UNIVEC reference or similar, you can do a BLAST search against common artificial sequences. https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/ ...
written 19 months ago by eric.kern13150
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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 2.0 years ago by eric.kern13150
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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 2.3 years ago by eric.kern13150
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Comment: C: Duplicated Reads In Rna-Seq Experiment
... (I would like to hear the answer to this as well.) ...
written 2.6 years ago by eric.kern13150
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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 2.6 years ago by eric.kern13150
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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 2.7 years ago by eric.kern13150 • updated 2.7 years ago by Santosh Anand5.0k
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Comment: C: Retrieve all genes under a mammalian phenotype ontology term
... Works like a charm. Thank you very much! ...
written 2.8 years ago by eric.kern13150

Latest awards to eric.kern13

Scholar 3 months ago, created an answer that has been accepted. For A: Looking for experience
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: How To Write Data In A Granges Object To A Bed File.
Popular Question 18 months ago, created a question with more than 1,000 views. For 1000 genomes technical data: match exon capture probes to samples
Popular Question 18 months ago, created a question with more than 1,000 views. For Read depths from 1000G exome sequencing are almost all zero.
Popular Question 19 months ago, created a question with more than 1,000 views. For Mappability Scores from bigWigAverageOverBed all zero
Popular Question 22 months ago, created a question with more than 1,000 views. For +/- strand conventions for probe sequences
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Pysam cannot find index
Supporter 2.3 years ago, voted at least 25 times.
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Pysam cannot find index
Scholar 3.4 years ago, created an answer that has been accepted. For A: Looking for experience
Scholar 4.5 years ago, created an answer that has been accepted. For A: Looking for experience
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Looking for experience

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