User: eric.kern13
eric.kern13 • 150
- Reputation:
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- United States
- Last seen:
- 3 months, 1 week ago
- Joined:
- 4 years, 6 months ago
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Posts by eric.kern13
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... 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.kern13 • 150
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... 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.kern13 • 150
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... Your link currently gives this thread as the first hit. Profit indeed. ...
written 16 months ago by
eric.kern13 • 150
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... 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.kern13 • 150
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... 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.kern13 • 150
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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.kern13 • 150
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... (I would like to hear the answer to this as well.) ...
written 2.6 years ago by
eric.kern13 • 150
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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 2.6 years ago by
eric.kern13 • 150
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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 2.7 years ago by
eric.kern13 • 150
• updated
2.7 years ago by
Santosh Anand ♦ 5.0k
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... Works like a charm. Thank you very much! ...
written 2.8 years ago by
eric.kern13 • 150
Latest awards to eric.kern13
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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.
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18 months ago,
created a question with more than 1,000 views.
For 1000 genomes technical data: match exon capture probes to samples
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18 months ago,
created a question with more than 1,000 views.
For Read depths from 1000G exome sequencing are almost all zero.
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19 months ago,
created a question with more than 1,000 views.
For Mappability Scores from bigWigAverageOverBed all zero
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22 months ago,
created a question with more than 1,000 views.
For +/- strand conventions for probe sequences
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2.0 years ago,
created a question with more than 1,000 views.
For Pysam cannot find index
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2.3 years ago,
voted at least 25 times.
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3.3 years ago,
created a question with more than 1,000 views.
For Pysam cannot find index
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