User: nkinney06

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nkinney0630
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Posts by nkinney06

<prev • 19 results • page 1 of 2 • next >
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Answer: A: cruzDB coordinates vs UCSC coordinates
... I'm surprised this question has received little attention as I am quite convinced there is an inconsistency in the cruzdb coordinate system; running the following code should be convincing enough. import cruzdb from cruzdb import Genome g = cruzdb.Genome('hg38') ########## ...
written 5 weeks ago by nkinney0630
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Comment: C: cruzDB coordinates vs UCSC coordinates
... Update: for anyone that uses cruzdb you may want to look into this unsolved issue. I received this comment from the developer: probably, these comparisons: https://github.com/brentp/cruzdb/blob/master/cruzdb/models.py#L81 need to use >= instead of >. If you verify that, I'll make ...
written 5 weeks ago by nkinney0630
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cruzDB coordinates vs UCSC coordinates
... I am confused by a subtle difference in the cruzdb coordinates and UCSC coordinates. For those unfamiliar cruzdb is a python package for accessing the UCSC databases. Suppose I am interested in exon 3/7 for the gene TAF3. This exon extends from base pair 7963920-7965742 on chromosome 10. You can be ...
python genome coordinates cruzdb ucsc written 6 weeks ago by nkinney0630 • updated 4 weeks ago by max10
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Comment: C: how to get cruzbd (cds_sequence) dna translation
... thank you! I have done both; but, I have a followup question. If we take another look at the region I used as an example: chromosome = "chr19" start = 55014736 stop = 55014753 and compare to the entry in the refGene.txt file from UCSC we see that this region is between the transcriptio ...
written 8 weeks ago by nkinney0630
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how to get cruzbd (cds_sequence) dna translation
... I have a genomic region of interest and I am trying to retrieve the gene (if its in one) and amino acid sequence (if its in a translated region). Suppose my region of interest is: chromosome = "chr19" start = 55014736 stop = 55014753 If I put this into USCS genome browser by hand I see it's in gen ...
python cruzdb written 9 weeks ago by nkinney0630 • updated 8 weeks ago by genecats.ucsc460
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brain scan databases
... I am wondering if there are any standard "brain scan" databases with data from fMRI, dMRI, sMRI, PET, CT scans etc for human. Im interested in addiction primarily, possible diabetes, heart disease, COPD, and anything that plausibly affects the brain. Ideally would be able to look up scans for these ...
imaging databases written 6 months ago by nkinney0630 • updated 6 months ago by Jean-Karim Heriche14k
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Comment: C: Use machine learning as classifier
... look up the pybrain tutorial on neural networks for classification ...
written 7 months ago by nkinney0630
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simple polygenic risk example
... I am trying to calculate polygenic risk scores. Basically these are calculated using a set of weighted SNPs. The score assigned to an individual can be correlated with many things such as risk for disease. Many polygenic risk scores (or models) have been devised and published in literature. I though ...
polygenic risk snp written 7 months ago by nkinney0630 • updated 7 months ago by Biostar ♦♦ 20
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transvar configuration and datafiles
... I am trying to install the reverse annotation program transvar: http://transvar.readthedocs.io/en/latest/download_and_install.html once you install with pip you have to configure by downloading the annotation files: > transvar config --download_anno --refversion hg19 when I run this command I ...
software error written 8 months ago by nkinney0630
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Comment: C: R not reading numbers from file
... Ill try but in reality my matrix will be rather large and the number of NAs would have to be dynamically assigned ...
written 8 months ago by nkinney0630

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