User: fongchunchan

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fongchunchan30
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New User
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Canada/Vancouver/BCCA
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http://tinyheero.githu...
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fongchunchan
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Last seen:
1 year ago
Joined:
2 years, 4 months ago
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Posts by fongchunchan

<prev • 6 results • page 1 of 1 • next >
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Comment: C: GEOquery Fails to Download Series Matrix File
... Thanks. That answers my question.  ...
written 12 months ago by fongchunchan30
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Answer: A: GEOquery Fails to Download Series Matrix File
... Thanks for the reply. I see. Any chance the conda package of bioconductor-geoquery can be updated with version 2.4? I've switched over to using conda for managing all my r package dependencies and the current version is only 2.38.4 on conda cloud hence explaining the problems... ...
written 12 months ago by fongchunchan30
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GEOquery Fails to Download Series Matrix File
... I am trying to use GEOquery to download the data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39133. Based on the vignette, I should be able to just run the code: gse <- getGEO('GSE39133') This produces the following output: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE391 ...
geoquery geo data ncbi geo written 12 months ago by fongchunchan30
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Suppressing the ID value from writeVcf
... Hi, I noticed that when I use VariantAnnotation::writeVcf() on a vcf file it will fill the ID column with a string that is the combination of chromosome, position, ref and alt allele. This happens even though the vcf file that I read in using VariantAnnotation::readVcf() had no values in the ID col ...
readvcf writevcf written 2.0 years ago by fongchunchan30 • updated 24 months ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: "Wobble" patterns for genome searching using Biostrings
... Yes this is exactly what I need. Thanks.  ...
written 2.4 years ago by fongchunchan30
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"Wobble" patterns for genome searching using Biostrings
... Hi, I've been going through the "Efficient genome searching with Biostrings and the BSgenome data packages" pdf document to get a grasp on how to search for a particular motif in a genome sequence. Specifically, I am interesting in looking for the RGYW motif. Which actually has a "wobble" (I think ...
bsgenome biostrings motif rgyw written 2.4 years ago by fongchunchan30

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