User: nkinney06

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nkinney0620
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Posts by nkinney06

<prev • 14 results • page 1 of 2 • next >
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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 3 months ago by nkinney0620 • updated 3 months ago by Jean-Karim Heriche13k
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Comment: C: Use machine learning as classifier
... look up the pybrain tutorial on neural networks for classification ...
written 4 months ago by nkinney0620
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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 4 months ago by nkinney0620 • updated 4 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 5 months ago by nkinney0620
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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 5 months ago by nkinney0620
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Answer: A: R not reading numbers from file
... That makes sense, but I appear to have the same problem when I run: similarityMatrix <- as.matrix( read.table( './testMatrix.txt', header=FALSE, sep = "\t", strip.white=TRUE, row.names = 1 ) ) I get: > similarityMatrix V2 V3 V4 V5 ...
written 5 months ago by nkinney0620
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R not reading numbers from file
... I am trying to read the following file into R variables: 5060803636482931868 83.3366666 0.0 0.0 0.0 15695800775901642752 0.0 81.0061726043 38.1837661841 0.0 12047011437325700351 0.0 38.1837661841 22.2036033112 7.07106781187 2610937148294873212 ...
R written 5 months ago by nkinney0620 • updated 5 months ago by h.mon9.2k
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Comment: C: why does this pipe work
... thanks but in this case if I type some-command 1>/dev/null it takes a very long time. However, if I type some-command | 1>/dev/null it finished very quickly. The pipe looks out of place to me but appears to work and I would like to know why. ...
written 6 months ago by nkinney0620
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why does this pipe work
... In looking for a way to check if a bamfile is truncated I noticed that this does the job very quickly. samtools view file.bam | 1>/dev/null The thing is I typed the pipe by accident; the command doesn't make sense to me but when you remove the pipe the command takes much longer (Im not sure it ...
software error bash written 6 months ago by nkinney0620 • updated 6 months ago by John12k
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(Closed) SNP coordinate conversion
... I am interested in converting the coordinates of SNP relative to their gene into a coordinate relative to the chromosome. For example; I have a SNP BRCA1 c.4327C>T I want to coordinates in the following form instead chr9:14801712 the reason is that litterature often uses the first convention ...
gene snp coordiantes written 7 months ago by nkinney0620

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