User: anastasiya-terskih

Reputation:
10
Status:
New User
Location:
Russian Federation
Last seen:
5 years, 1 month ago
Joined:
5 years, 2 months ago
Email:
a*****************@mail.ru

Posts by anastasiya-terskih

<prev • 7 results • page 1 of 1 • next >
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Comment: C: From rs IDs to NCBI dbSNP IDs
... Yes, it works!Thank you very much!   ...
written 5.2 years ago by anastasiya-terskih10
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Comment: C: From rs IDs to NCBI dbSNP IDs
... When I use rsids as  keys: si<-select(SIFT.Hsapiens.dbSNP137, keys=rsid, cols=subst1) , I can't find them in SIFT.Hsapiens.dbSNP137.  I have the message that there are not such keys in SIFT.Hsapiens.dbSNP137. Here is the message fron manual:  This package, SIFT.Hsapiens.dbSNP137, contains bot ...
written 5.2 years ago by anastasiya-terskih10
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From rs IDs to NCBI dbSNP IDs
... Hello!Could you help me, please. I need to use SIFT.Hsapiens.dbSNP137 instead of  SIFT.Hsapiens.dbSNP132. I have the list of rsIDs to use SIFT.Hsapiens.dbSNP132, but keys in SIFT.Hsapiens.dbSNP137 are NCBI dbSNP IDs. I don't know how i can find NCBI dbSNP IDs. Actually I used predictCoding() to g ...
sift rsids dbsnp written 5.2 years ago by anastasiya-terskih10 • updated 5.2 years ago by James W. MacDonald52k
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Comment: C: Overlap the snps
... Thank you very much!It works) ...
written 5.2 years ago by anastasiya-terskih10
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Overlap the snps
... Hello! Could you help me please. I use  predictCoding() to get information about nucleotide substitutions: > nonsyn <- predictCoding(vcf_mod, txdb, Hsapiens) Then I need to overlap the GRanges I've got from predictCoding() with the positition in the SNPloc package: > library(SNPlocs.H ...
iranges granges overlap snps written 5.2 years ago by anastasiya-terskih10 • updated 5.2 years ago by Michael Lawrence11k
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Comment: C: how to save file on local disk after applying predictCoding() function?
... Thank you very much!) ...
written 5.2 years ago by anastasiya-terskih10
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how to save file on local disk after applying predictCoding() function?
... Hello! Could you help me please. I work with vcf file: > vcf <- readVcf("test.vcf.gz", "hg19") Then I use  predictCoding() to get information about nucleotide substitutions and output looks like this: > coding <- predictCoding(vcf_mod, txdb, Hsapiens) > coding[5:7] GRanges with ...
variantannotation vcf predict coding save file written 5.2 years ago by anastasiya-terskih10 • updated 5.2 years ago by Thomas Sandmann70

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